From b1fee8a00318f4cf2cb3f854edc70f5c000ab71f Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 09:29:01 +0200 Subject: gnu: Add r-spp. * gnu/packages/bioinformatics.scm (r-spp): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9c77d66a35..bcc9f5bef2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8108,6 +8108,30 @@ (define-public r-seqpattern reference point and sorted by a user defined feature.") (license license:gpl3+))) +(define-public r-spp + (package + (name "r-spp") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (cran-uri "spp" version)) + (sha256 + (base32 + "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w")))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-catools" ,r-catools) + ("r-rcpp" ,r-rcpp) + ("r-rsamtools" ,r-rsamtools))) + (home-page "https://cran.r-project.org/web/packages/spp/") + (synopsis "ChIP-Seq processing pipeline") + (description "This package provides tools for analysis of ChIP-seq and +other functional sequencing data.") + (license license:gpl2))) + (define-public r-genomation (package (name "r-genomation") -- cgit v1.2.3 From af163badb409872b4c676ccb2274694ae892cc40 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 26 May 2021 09:34:37 +0200 Subject: gnu: Add r-phantompeakqualtools. * gnu/packages/bioinformatics.scm (r-phantompeakqualtools): New variable. --- gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bcc9f5bef2..074ff8046f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8132,6 +8132,53 @@ (define-public r-spp other functional sequencing data.") (license license:gpl2))) +(define-public r-phantompeakqualtools + (package + (name "r-phantompeakqualtools") + (version "1.2.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kundajelab/phantompeakqualtools") + (commit "8d2b2d18c686d894ef5908b37da7adf72a07ef42"))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "00anrvcwsp02d98qhj1xpj85644h2pp4kfzq6dgbmwmdr6jvy7p4")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests. + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((script (string-append (assoc-ref outputs "out") + "/share/scripts"))) + (install-file "run_spp.R" script))))))) + (inputs + `(("r" ,r-minimal))) + (propagated-inputs + `(("r-catools" ,r-catools) + ("r-snow" ,r-snow) + ("r-snowfall" ,r-snowfall) + ("r-bitops" ,r-bitops) + ("r-rsamtools" ,r-rsamtools) + ("r-spp" ,r-spp) + ("gawk" ,gawk) + ("samtools" ,samtools) + ("boost" ,boost) + ("gzip" ,gzip))) + (home-page "https://github.com/kundajelab/phantompeakqualtools") + (synopsis "Informative enrichment for ChIP-seq data") + (description "This package computes informative enrichment and quality +measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be +used to obtain robust estimates of the predominant fragment length or +characteristic tag shift values in these assays.") + (license license:bsd-3))) + (define-public r-genomation (package (name "r-genomation") -- cgit v1.2.3 From 36a90d0637bb47b113ceda5abb64c50600837436 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 26 May 2021 13:40:59 +0300 Subject: gnu: minimap2: Update to 2.18. * gnu/packages/bioinformatics.scm (minimap2): Update to 2.18. [source]: Remove patch. * gnu/packages/patches/minimap2-aarch64-support.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 5 +-- .../patches/minimap2-aarch64-support.patch | 52 ---------------------- 3 files changed, 2 insertions(+), 56 deletions(-) delete mode 100644 gnu/packages/patches/minimap2-aarch64-support.patch (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/local.mk b/gnu/local.mk index b0df9d582d..8355a208ea 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1424,7 +1424,6 @@ dist_patch_DATA = \ %D%/packages/patches/mingw-w64-6.0.0-gcc.patch \ %D%/packages/patches/mingw-w64-dlltool-temp-prefix.patch \ %D%/packages/patches/mingw-w64-reproducible-gendef.patch \ - %D%/packages/patches/minimap2-aarch64-support.patch \ %D%/packages/patches/minisat-friend-declaration.patch \ %D%/packages/patches/minisat-install.patch \ %D%/packages/patches/mit-krb5-hurd.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 074ff8046f..46092fd589 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12323,7 +12323,7 @@ (define-public sjcount (define-public minimap2 (package (name "minimap2") - (version "2.17") + (version "2.18") (source (origin (method url-fetch) @@ -12332,8 +12332,7 @@ (define-public minimap2 "minimap2-" version ".tar.bz2")) (sha256 (base32 - "0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn")) - (patches (search-patches "minimap2-aarch64-support.patch")))) + "1d7fvdqcqd6wns875rkyd7f34ii15gc9l1sivd2wbbpcb0fi0mbs")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are none diff --git a/gnu/packages/patches/minimap2-aarch64-support.patch b/gnu/packages/patches/minimap2-aarch64-support.patch deleted file mode 100644 index 95db8579d6..0000000000 --- a/gnu/packages/patches/minimap2-aarch64-support.patch +++ /dev/null @@ -1,52 +0,0 @@ -This patch should be removed with the next release. There is WIP upstream -support for proper support of more architectures, including aarch64 and powerpc64le. - -diff --git a/Makefile b/Makefile -index ed341f6..94dbd85 100644 ---- a/Makefile -+++ b/Makefile -@@ -6,20 +6,18 @@ PROG= minimap2 - PROG_EXTRA= sdust minimap2-lite - LIBS= -lm -lz -lpthread - --ifeq ($(arm_neon),) # if arm_neon is not defined --ifeq ($(sse2only),) # if sse2only is not defined -- OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o --else # if sse2only is defined -- OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o --endif --else # if arm_neon is defined -+ifneq ($(arm_neon),) # if arm_neon is defined - OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o -- INCLUDES+=-Isse2neon --ifeq ($(aarch64),) #if aarch64 is not defined - CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char --else #if aarch64 is defined -+ INCLUDES+=-Isse2neon -+else ifneq ($(aarch64),) #if aarch64 is defined -+ OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o - CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char --endif -+ INCLUDES+=-Isse2neon -+else ifneq ($(sse2only),) # if sse2only is defined -+ OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o -+else # none of the above -+ OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o - endif - - .PHONY:all extra clean depend -@@ -46,9 +44,12 @@ sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h - - # SSE-specific targets on x86/x86_64 - --ifeq ($(arm_neon),) # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2) -+ifneq ($(arm_neon),) # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2) -+ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h -+else ifneq ($(aarch64),) - ksw2_ll_sse.o:ksw2_ll_sse.c ksw2.h kalloc.h -- $(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@ -+else -+ $(CC) -c $(CFLAGS) -msse2 $(CPPFLAGS) $(INCLUDES) $< -o $@ - endif - - ksw2_extz2_sse41.o:ksw2_extz2_sse.c ksw2.h kalloc.h -- cgit v1.2.3 From c5f7203e3eea9453c773f7e38c4adc50f09b024c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 26 May 2021 13:42:26 +0300 Subject: gnu: minimap2: Install more files. * gnu/packages/bioinformatics.scm (minimap2)[arguments]: Add modules. Adjust custom 'install phase to also install library, headers and a pkg-config file. --- gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++-- 1 file changed, 25 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 46092fd589..af1010f853 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12336,6 +12336,9 @@ (define-public minimap2 (build-system gnu-build-system) (arguments `(#:tests? #f ; there are none + #:modules ((guix build utils) + (guix build gnu-build-system) + (srfi srfi-26)) #:make-flags (list (string-append "CC=" ,(cc-for-target)) (let ((system ,(or (%current-target-system) @@ -12358,10 +12361,30 @@ (define-public minimap2 (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin")) + (lib (string-append out "/lib")) + (inc (string-append out "/include")) (man (string-append out "/share/man/man1"))) (install-file "minimap2" bin) - (mkdir-p man) - (install-file "minimap2.1" man)) + (install-file "libminimap2.a" lib) + (install-file "minimap2.1" man) + (map (cut install-file <> inc) + (find-files "." "\\.h$")) + ;; Not this file. + (delete-file (string-append inc "/emmintrin.h")) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/minimap2.pc") + (lambda _ + (format #t "prefix=~a~@ + exec_prefix=${prefix}~@ + libdir=${exec_prefix}/lib~@ + includedir=${prefix}/include~@ + ~@ + Name: libminimap2~@ + Version: ~a~@ + Description: A versatile pairwise aligner for genomic and spliced nucleotide sequence~@ + Libs: -L${libdir} -lminimap2~@ + Cflags: -I${includedir}~%" + out ,version)))) #t))))) (inputs `(("zlib" ,zlib))) -- cgit v1.2.3 From a30e616cccc850f0c9ad809be7db82729f46d0d8 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 27 May 2021 22:50:46 +0200 Subject: gnu: Add python-htsget. * gnu/packages/bioinformatics.scm (python-htsget): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index af1010f853..6f3bc96c9e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -846,6 +846,30 @@ (define-public bioawk intended to behave exactly the same as the original BWK awk.") (license license:x11))) +(define-public python-htsget + (package + (name "python-htsget") + (version "0.2.5") + (source (origin + (method url-fetch) + (uri (pypi-uri "htsget" version)) + (sha256 + (base32 + "0ic07q85vhw9djf23k57b21my7i5xp400m8gfqgr5gcryqvdr0yk")))) + (build-system python-build-system) + (native-inputs + `(("python-setuptools-scm" ,python-setuptools-scm))) + (propagated-inputs + `(("python-humanize" ,python-humanize) + ("python-requests" ,python-requests) + ("python-six" ,python-six))) + (home-page "https://pypi.org/project/htsget/") + (synopsis "Python API and command line interface for the GA4GH htsget API") + (description "This package is a client implementation of the GA4GH htsget +protocol. It provides a simple and reliable way to retrieve genomic data from +servers supporting the protocol.") + (license license:asl2.0))) + (define-public python-pybedtools (package (name "python-pybedtools") -- cgit v1.2.3 From 87c9f63fce05063c190e277a8d79803fa3693e11 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 27 May 2021 23:01:35 +0200 Subject: gnu: Add python-pyega3. * gnu/packages/bioinformatics.scm (python-pyega3): New variable. --- gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6f3bc96c9e..f38c0c07ef 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1994,6 +1994,45 @@ (define-public python-bx-python (define-public python2-bx-python (package-with-python2 python-bx-python)) +(define-public python-pyega3 + (package + (name "python-pyega3") + (version "3.4.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "pyega3" version)) + (sha256 + (base32 + "1k736in8g27rarx65ym9xk50x53zjg75h37bb8ljynxv04rypx2q")))) + (build-system python-build-system) + (arguments + `(#:tests? #f)) ; The tests require network access. + (native-inputs + `(("python-psutil" ,python-psutil) + ("python-htsget" ,python-htsget))) + (propagated-inputs + `(("python-requests" ,python-requests) + ("python-tqdm" ,python-tqdm) + ("python-urllib3" ,python-urllib3) + ("python-responses" ,python-responses))) + (home-page "https://github.com/EGA-archive/ega-download-client") + (synopsis "Python client for EGA") + (description "This package is a python-based tool for viewing and +downloading files from authorized EGA datasets. It uses the EGA data API and +has several key features: +@itemize +@item Files are transferred over secure https connections and received + unencrypted, so no need for decryption after download. +@item Downloads resume from where they left off in the event that the + connection is interrupted. +@item Supports file segmenting and parallelized download of segments, + improving overall performance. +@item After download completes, file integrity is verified using checksums. +@item Implements the GA4GH-compliant htsget protocol for download of genomic + ranges for data files with accompanying index files. +@end itemize\n") + (license license:asl2.0))) + (define-public python-pysam (package (name "python-pysam") -- cgit v1.2.3 From b1ae0f30d856503fa311d380584a6d7c80559332 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 28 May 2021 17:33:37 +0200 Subject: gnu: Add mosaicatcher. * gnu/packages/bioinformatics.scm (mosaicatcher): New variable. --- gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f38c0c07ef..2a7443314a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6170,6 +6170,46 @@ (define-public mosaik ;; 2. MD5 implementation - RSA Data Security, RFC 1321 (license (list license:gpl2+ license:public-domain))))) +(define-public mosaicatcher + (package + (name "mosaicatcher") + (version "0.3.1") + (source (origin + ;; There are no release tarballs nor tags. + (method git-fetch) + (uri (git-reference + (url "https://github.com/friendsofstrandseq/mosaicatcher") + (commit (string-append version "-dev")))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1n2s5wvvj2y0vfgjkg1q11xahpbagxz7h2vf5q7qyy25s12kbzbd")) + (patches (search-patches "mosaicatcher-unbundle-htslib.patch")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #false ; there are no tests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "src"))) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((target (assoc-ref outputs "out")) + (bin (string-append target "/bin")) + (share (string-append target "/share/mosaicatcher"))) + (install-file "mosaic" bin) + (mkdir-p share) + (copy-recursively "../R" share))))))) + (inputs + `(("boost" ,boost) + ("htslib" ,htslib))) + (home-page "https://github.com/friendsofstrandseq/mosaicatcher") + (synopsis "Count and classify Strand-seq reads") + (description + "Mosaicatcher counts Strand-seq reads and classifies strand states of +each chromosome in each cell using a Hidden Markov Model.") + (license license:expat))) + (define-public ngs-sdk (package (name "ngs-sdk") -- cgit v1.2.3 From 6417b97c7e10de8592ac9fda15774ee711d3dc25 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sat, 29 May 2021 01:21:14 +0100 Subject: Revert "gnu: Add mosaicatcher." mosaicatcher-unbundle-htslib.patch is missing. This reverts commit b1ae0f30d856503fa311d380584a6d7c80559332. --- gnu/packages/bioinformatics.scm | 40 ---------------------------------------- 1 file changed, 40 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2a7443314a..f38c0c07ef 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6170,46 +6170,6 @@ (define-public mosaik ;; 2. MD5 implementation - RSA Data Security, RFC 1321 (license (list license:gpl2+ license:public-domain))))) -(define-public mosaicatcher - (package - (name "mosaicatcher") - (version "0.3.1") - (source (origin - ;; There are no release tarballs nor tags. - (method git-fetch) - (uri (git-reference - (url "https://github.com/friendsofstrandseq/mosaicatcher") - (commit (string-append version "-dev")))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1n2s5wvvj2y0vfgjkg1q11xahpbagxz7h2vf5q7qyy25s12kbzbd")) - (patches (search-patches "mosaicatcher-unbundle-htslib.patch")))) - (build-system cmake-build-system) - (arguments - `(#:tests? #false ; there are no tests - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'chdir - (lambda _ (chdir "src"))) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((target (assoc-ref outputs "out")) - (bin (string-append target "/bin")) - (share (string-append target "/share/mosaicatcher"))) - (install-file "mosaic" bin) - (mkdir-p share) - (copy-recursively "../R" share))))))) - (inputs - `(("boost" ,boost) - ("htslib" ,htslib))) - (home-page "https://github.com/friendsofstrandseq/mosaicatcher") - (synopsis "Count and classify Strand-seq reads") - (description - "Mosaicatcher counts Strand-seq reads and classifies strand states of -each chromosome in each cell using a Hidden Markov Model.") - (license license:expat))) - (define-public ngs-sdk (package (name "ngs-sdk") -- cgit v1.2.3 From e3cde9aaf8dfef17299987590db11aa1f4df418b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 29 May 2021 07:25:08 +0200 Subject: gnu: Add mosaicatcher. * gnu/packages/patches/mosaicatcher-unbundle-htslib.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/bioinformatics.scm (mosaicatcher): New variable. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++ .../patches/mosaicatcher-unbundle-htslib.patch | 49 ++++++++++++++++++++++ 3 files changed, 90 insertions(+) create mode 100644 gnu/packages/patches/mosaicatcher-unbundle-htslib.patch (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/local.mk b/gnu/local.mk index 792ebac1e1..cf13d672bd 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1432,6 +1432,7 @@ dist_patch_DATA = \ %D%/packages/patches/module-init-tools-moduledir.patch \ %D%/packages/patches/monero-use-system-miniupnpc.patch \ %D%/packages/patches/mono-mdoc-timestamping.patch \ + %D%/packages/patches/mosaicatcher-unbundle-htslib.patch \ %D%/packages/patches/mozjs17-aarch64-support.patch \ %D%/packages/patches/mozjs24-aarch64-support.patch \ %D%/packages/patches/mozjs38-pkg-config-version.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f38c0c07ef..2a7443314a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6170,6 +6170,46 @@ (define-public mosaik ;; 2. MD5 implementation - RSA Data Security, RFC 1321 (license (list license:gpl2+ license:public-domain))))) +(define-public mosaicatcher + (package + (name "mosaicatcher") + (version "0.3.1") + (source (origin + ;; There are no release tarballs nor tags. + (method git-fetch) + (uri (git-reference + (url "https://github.com/friendsofstrandseq/mosaicatcher") + (commit (string-append version "-dev")))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1n2s5wvvj2y0vfgjkg1q11xahpbagxz7h2vf5q7qyy25s12kbzbd")) + (patches (search-patches "mosaicatcher-unbundle-htslib.patch")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #false ; there are no tests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "src"))) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((target (assoc-ref outputs "out")) + (bin (string-append target "/bin")) + (share (string-append target "/share/mosaicatcher"))) + (install-file "mosaic" bin) + (mkdir-p share) + (copy-recursively "../R" share))))))) + (inputs + `(("boost" ,boost) + ("htslib" ,htslib))) + (home-page "https://github.com/friendsofstrandseq/mosaicatcher") + (synopsis "Count and classify Strand-seq reads") + (description + "Mosaicatcher counts Strand-seq reads and classifies strand states of +each chromosome in each cell using a Hidden Markov Model.") + (license license:expat))) + (define-public ngs-sdk (package (name "ngs-sdk") diff --git a/gnu/packages/patches/mosaicatcher-unbundle-htslib.patch b/gnu/packages/patches/mosaicatcher-unbundle-htslib.patch new file mode 100644 index 0000000000..262895ddcf --- /dev/null +++ b/gnu/packages/patches/mosaicatcher-unbundle-htslib.patch @@ -0,0 +1,49 @@ +--- a/src/CMakeLists.txt 2021-05-28 13:07:25.655107983 +0200 ++++ b/src/CMakeLists.txt 2021-05-28 13:09:55.764025497 +0200 +@@ -21,24 +21,6 @@ + + + +-### Link HTSlib +- +-ExternalProject_Add(htslib +- PREFIX ${CMAKE_BINARY_DIR}/htslib +- GIT_REPOSITORY "https://github.com/samtools/htslib.git" +- GIT_TAG "1.3.1" +- UPDATE_COMMAND "" +- BUILD_IN_SOURCE 1 +- CONFIGURE_COMMAND "" +- BUILD_COMMAND make +- INSTALL_COMMAND make install prefix=${CMAKE_BINARY_DIR}/htslib +- LOG_DOWNLOAD 1 +-) +-link_directories (${CMAKE_BINARY_DIR}/htslib/lib) +-include_directories (${CMAKE_BINARY_DIR}/htslib/include) +- +- +- + ### Set version + + # Get the current working branch +@@ -64,13 +46,6 @@ + + # 2. Boost version from find_package (Boost_VERSION) + +-# 3. Get HTSlib version from git +-execute_process( +- COMMAND git describe --always +- WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/htslib +- OUTPUT_VARIABLE HTSLIB_VERSION +- OUTPUT_STRIP_TRAILING_WHITESPACE +-) + set(HTSLIB_VERSION "1.3.1 ${HTSLIB_VERSION}") + + # 4. write version.hpp file +@@ -105,7 +80,6 @@ + add_executable (mosaic main.cpp ${HEADER_FILES}) + target_link_libraries (mosaic LINK_PUBLIC ${Boost_LIBRARIES}) + target_link_libraries (mosaic LINK_PUBLIC hts) +-add_dependencies (mosaic htslib) + + + ### Doxygen API documentation -- cgit v1.2.3 From ca1a015777565f1098d56ac3b5873226e50c067d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:33 +0200 Subject: gnu: r-genomicalignments: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-genomicalignments): Move from here... * gnu/packages/bioconductor.scm (r-genomicalignments): ...to here. --- gnu/packages/bioconductor.scm | 35 ++++++++++++++++++++++++++++++++++- gnu/packages/bioinformatics.scm | 33 --------------------------------- 2 files changed, 34 insertions(+), 34 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b58c5bc11f..eef0811d4e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft @@ -2280,6 +2280,39 @@ (define-public r-genomeinfodb names in their natural, rather than lexicographic, order.") (license license:artistic2.0))) +(define-public r-genomicalignments + (package + (name "r-genomicalignments") + (version "1.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicAlignments" version)) + (sha256 + (base32 + "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr")))) + (properties + `((upstream-name . "GenomicAlignments"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/GenomicAlignments") + (synopsis "Representation and manipulation of short genomic alignments") + (description + "This package provides efficient containers for storing and manipulating +short genomic alignments (typically obtained by aligning short reads to a +reference genome). This includes read counting, computing the coverage, +junction detection, and working with the nucleotide content of the +alignments.") + (license license:artistic2.0))) + (define-public r-genomicranges (package (name "r-genomicranges") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2a7443314a..ba284759a0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7952,39 +7952,6 @@ (define-public bio-vcf (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomicalignments - (package - (name "r-genomicalignments") - (version "1.26.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicAlignments" version)) - (sha256 - (base32 - "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr")))) - (properties - `((upstream-name . "GenomicAlignments"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (home-page "https://bioconductor.org/packages/GenomicAlignments") - (synopsis "Representation and manipulation of short genomic alignments") - (description - "This package provides efficient containers for storing and manipulating -short genomic alignments (typically obtained by aligning short reads to a -reference genome). This includes read counting, computing the coverage, -junction detection, and working with the nucleotide content of the -alignments.") - (license license:artistic2.0))) - (define-public r-rtracklayer (package (name "r-rtracklayer") -- cgit v1.2.3 From a88230a1bc332ee41eb1e0080f020e0178f78d5a Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:34 +0200 Subject: gnu: r-rtracklayer: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-rtracklayer): Move from here... * gnu/packages/bioconductor.scm (r-rtracklayer): ...to here. --- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 48 ----------------------------------------- 2 files changed, 48 insertions(+), 48 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eef0811d4e..2b3c232d53 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2590,6 +2590,54 @@ (define-public r-rsamtools tab-delimited (tabix) files.") (license license:expat))) +(define-public r-rtracklayer + (package + (name "r-rtracklayer") + (version "1.50.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "rtracklayer" version)) + (sha256 + (base32 + "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-zlib + (lambda _ + (substitute* "DESCRIPTION" + ((" zlibbioc,") "")) + (substitute* "NAMESPACE" + (("import\\(zlibbioc\\)") "")) + #t))))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-xml" ,r-xml) + ("r-xvector" ,r-xvector) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/rtracklayer") + (synopsis "R interface to genome browsers and their annotation tracks") + (description + "rtracklayer is an extensible framework for interacting with multiple +genome browsers (currently UCSC built-in) and manipulating annotation tracks +in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit +built-in). The user may export/import tracks to/from the supported browsers, +as well as query and modify the browser state, such as the current viewport.") + (license license:artistic2.0))) + (define-public r-shortread (package (name "r-shortread") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ba284759a0..f9d2d125bf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7952,54 +7952,6 @@ (define-public bio-vcf (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-rtracklayer - (package - (name "r-rtracklayer") - (version "1.50.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "rtracklayer" version)) - (sha256 - (base32 - "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8")))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-system-zlib - (lambda _ - (substitute* "DESCRIPTION" - ((" zlibbioc,") "")) - (substitute* "NAMESPACE" - (("import\\(zlibbioc\\)") "")) - #t))))) - (native-inputs - `(("pkg-config" ,pkg-config))) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) - (home-page "https://bioconductor.org/packages/rtracklayer") - (synopsis "R interface to genome browsers and their annotation tracks") - (description - "rtracklayer is an extensible framework for interacting with multiple -genome browsers (currently UCSC built-in) and manipulating annotation tracks -in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit -built-in). The user may export/import tracks to/from the supported browsers, -as well as query and modify the browser state, such as the current viewport.") - (license license:artistic2.0))) - (define-public r-genomicfeatures (package (name "r-genomicfeatures") -- cgit v1.2.3 From f78ff75b411fe2d07b18529db6fb1da231bcc4cd Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:35 +0200 Subject: gnu: r-genomicfeatures: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-genomicfeatures): Move from here... * gnu/packages/bioconductor.scm (r-genomicfeatures): ...to here. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 43 ----------------------------------------- 2 files changed, 43 insertions(+), 43 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2b3c232d53..7278bb486b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2313,6 +2313,49 @@ (define-public r-genomicalignments alignments.") (license license:artistic2.0))) +(define-public r-genomicfeatures + (package + (name "r-genomicfeatures") + (version "1.42.3") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicFeatures" version)) + (sha256 + (base32 + "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz")))) + (properties + `((upstream-name . "GenomicFeatures"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/GenomicFeatures") + (synopsis "Tools for working with transcript centric annotations") + (description + "This package provides a set of tools and methods for making and +manipulating transcript centric annotations. With these tools the user can +easily download the genomic locations of the transcripts, exons and cds of a +given organism, from either the UCSC Genome Browser or a BioMart +database (more sources will be supported in the future). This information is +then stored in a local database that keeps track of the relationship between +transcripts, exons, cds and genes. Flexible methods are provided for +extracting the desired features in a convenient format.") + (license license:artistic2.0))) + (define-public r-genomicranges (package (name "r-genomicranges") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f9d2d125bf..fe81959ef0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7952,49 +7952,6 @@ (define-public bio-vcf (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomicfeatures - (package - (name "r-genomicfeatures") - (version "1.42.3") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicFeatures" version)) - (sha256 - (base32 - "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz")))) - (properties - `((upstream-name . "GenomicFeatures"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/GenomicFeatures") - (synopsis "Tools for working with transcript centric annotations") - (description - "This package provides a set of tools and methods for making and -manipulating transcript centric annotations. With these tools the user can -easily download the genomic locations of the transcripts, exons and cds of a -given organism, from either the UCSC Genome Browser or a BioMart -database (more sources will be supported in the future). This information is -then stored in a local database that keeps track of the relationship between -transcripts, exons, cds and genes. Flexible methods are provided for -extracting the desired features in a convenient format.") - (license license:artistic2.0))) - (define-public r-go-db (package (name "r-go-db") -- cgit v1.2.3 From 90bbab5cff337c522003adde870f127179f25f3d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:36 +0200 Subject: gnu: r-topgo: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-topgo): Move from here... * gnu/packages/bioconductor.scm (r-topgo): ...to here. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 33 --------------------------------- 2 files changed, 33 insertions(+), 33 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7278bb486b..a0f5222937 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2873,6 +2873,39 @@ (define-public r-systempiper annotation infrastructure.") (license license:artistic2.0))) +(define-public r-topgo + (package + (name "r-topgo") + (version "2.42.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "topGO" version)) + (sha256 + (base32 + "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl")))) + (properties + `((upstream-name . "topGO"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-dbi" ,r-dbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-go-db" ,r-go-db) + ("r-graph" ,r-graph) + ("r-lattice" ,r-lattice) + ("r-matrixstats" ,r-matrixstats) + ("r-sparsem" ,r-sparsem))) + (home-page "https://bioconductor.org/packages/topGO") + (synopsis "Enrichment analysis for gene ontology") + (description + "The topGO package provides tools for testing @dfn{gene ontology} (GO) +terms while accounting for the topology of the GO graph. Different test +statistics and different methods for eliminating local similarities and +dependencies between GO terms can be implemented and applied.") + ;; Any version of the LGPL applies. + (license license:lgpl2.1+))) + (define-public r-variantannotation (package (name "r-variantannotation") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fe81959ef0..e78769b1d3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7976,39 +7976,6 @@ (define-public r-go-db information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-topgo - (package - (name "r-topgo") - (version "2.42.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "topGO" version)) - (sha256 - (base32 - "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl")))) - (properties - `((upstream-name . "topGO"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dbi" ,r-dbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-lattice" ,r-lattice) - ("r-matrixstats" ,r-matrixstats) - ("r-sparsem" ,r-sparsem))) - (home-page "https://bioconductor.org/packages/topGO") - (synopsis "Enrichment analysis for gene ontology") - (description - "The topGO package provides tools for testing @dfn{gene ontology} (GO) -terms while accounting for the topology of the GO graph. Different test -statistics and different methods for eliminating local similarities and -dependencies between GO terms can be implemented and applied.") - ;; Any version of the LGPL applies. - (license license:lgpl2.1+))) - (define-public r-bsgenome (package (name "r-bsgenome") -- cgit v1.2.3 From 537d48d8695cf54da8957277aaac12b3991167c8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:37 +0200 Subject: gnu: r-bsgenome: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-bsgenome): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome): ...to here. --- gnu/packages/bioconductor.scm | 33 ++++++++++++++++++++++++++++++++- gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 32 insertions(+), 32 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a0f5222937..5825a69d18 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017 Efraim Flashner -;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu @@ -2080,6 +2080,37 @@ (define-public r-biostrings biological sequences or sets of sequences.") (license license:artistic2.0))) +(define-public r-bsgenome + (package + (name "r-bsgenome") + (version "1.58.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome" version)) + (sha256 + (base32 + "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq")))) + (properties + `((upstream-name . "BSgenome"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/BSgenome") + (synopsis "Infrastructure for Biostrings-based genome data packages") + (description + "This package provides infrastructure shared by all Biostrings-based +genome data packages and support for efficient SNP representation.") + (license license:artistic2.0))) + (define-public r-category (package (name "r-category") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e78769b1d3..7a55ebd559 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7976,37 +7976,6 @@ (define-public r-go-db information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-bsgenome - (package - (name "r-bsgenome") - (version "1.58.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "BSgenome" version)) - (sha256 - (base32 - "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq")))) - (properties - `((upstream-name . "BSgenome"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (home-page "https://bioconductor.org/packages/BSgenome") - (synopsis "Infrastructure for Biostrings-based genome data packages") - (description - "This package provides infrastructure shared by all Biostrings-based -genome data packages and support for efficient SNP representation.") - (license license:artistic2.0))) - (define-public r-impute (package (name "r-impute") -- cgit v1.2.3 From 8c7c78bfced859bc636752b03384f7f380398f71 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:38 +0200 Subject: gnu: r-msnid: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-msnid): Move from here... * gnu/packages/bioconductor.scm (r-msnid): ...to here. --- gnu/packages/bioconductor.scm | 52 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 52 ----------------------------------------- 2 files changed, 52 insertions(+), 52 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5825a69d18..f16e01261a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2517,6 +2517,58 @@ (define-public r-limma different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-msnid + (package + (name "r-msnid") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MSnID" version)) + (sha256 + (base32 + "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d")))) + (properties `((upstream-name . "MSnID"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationhub" ,r-annotationhub) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocstyle" ,r-biocstyle) + ("r-biostrings" ,r-biostrings) + ("r-data-table" ,r-data-table) + ("r-doparallel" ,r-doparallel) + ("r-dplyr" ,r-dplyr) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-iterators" ,r-iterators) + ("r-msnbase" ,r-msnbase) + ("r-msmstests" ,r-msmstests) + ("r-mzid" ,r-mzid) + ("r-mzr" ,r-mzr) + ("r-protgenerics" ,r-protgenerics) + ("r-purrr" ,r-purrr) + ("r-r-cache" ,r-r-cache) + ("r-rcpp" ,r-rcpp) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) + ("r-runit" ,r-runit) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-xtable" ,r-xtable))) + (home-page "https://bioconductor.org/packages/MSnID") + (synopsis "Utilities for LC-MSn proteomics identifications") + (description + "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data +from mzIdentML (leveraging the mzID package) or text files. After collating +the search results from multiple datasets it assesses their identification +quality and optimize filtering criteria to achieve the maximum number of +identifications while not exceeding a specified false discovery rate. It also +contains a number of utilities to explore the MS/MS results and assess missed +and irregular enzymatic cleavages, mass measurement accuracy, etc.") + (license license:artistic2.0))) + (define-public r-rbgl (package (name "r-rbgl") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7a55ebd559..478de5634e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9449,58 +9449,6 @@ (define-public r-msnbase of mass spectrometry based proteomics data.") (license license:artistic2.0))) -(define-public r-msnid - (package - (name "r-msnid") - (version "1.24.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "MSnID" version)) - (sha256 - (base32 - "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d")))) - (properties `((upstream-name . "MSnID"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocstyle" ,r-biocstyle) - ("r-biostrings" ,r-biostrings) - ("r-data-table" ,r-data-table) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-iterators" ,r-iterators) - ("r-msnbase" ,r-msnbase) - ("r-msmstests" ,r-msmstests) - ("r-mzid" ,r-mzid) - ("r-mzr" ,r-mzr) - ("r-protgenerics" ,r-protgenerics) - ("r-purrr" ,r-purrr) - ("r-r-cache" ,r-r-cache) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-runit" ,r-runit) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-xtable" ,r-xtable))) - (home-page "https://bioconductor.org/packages/MSnID") - (synopsis "Utilities for LC-MSn proteomics identifications") - (description - "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data -from mzIdentML (leveraging the mzID package) or text files. After collating -the search results from multiple datasets it assesses their identification -quality and optimize filtering criteria to achieve the maximum number of -identifications while not exceeding a specified false discovery rate. It also -contains a number of utilities to explore the MS/MS results and assess missed -and irregular enzymatic cleavages, mass measurement accuracy, etc.") - (license license:artistic2.0))) - (define-public r-aroma-light (package (name "r-aroma-light") -- cgit v1.2.3 From 4f030cc0db4806def4bb434817daee0e6c1cfa7d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:39 +0200 Subject: gnu: r-msnbase: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-msnbase): Move from here... * gnu/packages/bioconductor.scm (r-msnbase): ...to here. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 45 ----------------------------------------- 2 files changed, 45 insertions(+), 45 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f16e01261a..0db6590be3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2517,6 +2517,51 @@ (define-public r-limma different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-msnbase + (package + (name "r-msnbase") + (version "2.16.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MSnbase" version)) + (sha256 + (base32 + "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h")))) + (properties `((upstream-name . "MSnbase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-digest" ,r-digest) + ("r-ggplot2" ,r-ggplot2) + ("r-impute" ,r-impute) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-maldiquant" ,r-maldiquant) + ("r-mass" ,r-mass) + ("r-mzid" ,r-mzid) + ("r-mzr" ,r-mzr) + ("r-pcamethods" ,r-pcamethods) + ("r-plyr" ,r-plyr) + ("r-preprocesscore" ,r-preprocesscore) + ("r-protgenerics" ,r-protgenerics) + ("r-rcpp" ,r-rcpp) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-vsn" ,r-vsn) + ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/lgatto/MSnbase") + (synopsis "Base functions and classes for MS-based proteomics") + (description + "This package provides basic plotting, data manipulation and processing +of mass spectrometry based proteomics data.") + (license license:artistic2.0))) + (define-public r-msnid (package (name "r-msnid") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 478de5634e..e402efa4ad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9404,51 +9404,6 @@ (define-public r-pcamethods structure (pcaRes) to provide a common interface to the PCA results.") (license license:gpl3+))) -(define-public r-msnbase - (package - (name "r-msnbase") - (version "2.16.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "MSnbase" version)) - (sha256 - (base32 - "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h")))) - (properties `((upstream-name . "MSnbase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-digest" ,r-digest) - ("r-ggplot2" ,r-ggplot2) - ("r-impute" ,r-impute) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-maldiquant" ,r-maldiquant) - ("r-mass" ,r-mass) - ("r-mzid" ,r-mzid) - ("r-mzr" ,r-mzr) - ("r-pcamethods" ,r-pcamethods) - ("r-plyr" ,r-plyr) - ("r-preprocesscore" ,r-preprocesscore) - ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-vsn" ,r-vsn) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/lgatto/MSnbase") - (synopsis "Base functions and classes for MS-based proteomics") - (description - "This package provides basic plotting, data manipulation and processing -of mass spectrometry based proteomics data.") - (license license:artistic2.0))) - (define-public r-aroma-light (package (name "r-aroma-light") -- cgit v1.2.3 From b832fddbfc83dfc1b13a4f113a9d3f86754e4c57 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:41 +0200 Subject: gnu: r-impute: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-impute): Move from here... * gnu/packages/bioconductor.scm (r-impute): ...to here. --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ gnu/packages/bioinformatics.scm | 20 -------------------- 2 files changed, 20 insertions(+), 20 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9c6ba94838..a4a3fbd39a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2499,6 +2499,26 @@ (define-public r-hpar the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-impute + (package + (name "r-impute") + (version "1.64.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "impute" version)) + (sha256 + (base32 + "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa")))) + (native-inputs + `(("gfortran" ,gfortran))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/impute") + (synopsis "Imputation for microarray data") + (description + "This package provides a function to impute missing gene expression +microarray data, using nearest neighbor averaging.") + (license license:gpl2+))) + (define-public r-limma (package (name "r-limma") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e402efa4ad..566370c37f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7976,26 +7976,6 @@ (define-public r-go-db information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-impute - (package - (name "r-impute") - (version "1.64.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "impute" version)) - (sha256 - (base32 - "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa")))) - (native-inputs - `(("gfortran" ,gfortran))) - (build-system r-build-system) - (home-page "https://bioconductor.org/packages/impute") - (synopsis "Imputation for microarray data") - (description - "This package provides a function to impute missing gene expression -microarray data, using nearest neighbor averaging.") - (license license:gpl2+))) - (define-public r-seqpattern (package (name "r-seqpattern") -- cgit v1.2.3 From 14fb30e5f68dca6c64508ce3accce0a1722b118b Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:42 +0200 Subject: gnu: r-seqpattern: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-seqpattern): Move from here... * gnu/packages/bioconductor.scm (r-seqpattern): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a4a3fbd39a..d386f2270e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2860,6 +2860,33 @@ (define-public r-samr ;; Any version of the LGPL (license license:lgpl3+))) +(define-public r-seqpattern + (package + (name "r-seqpattern") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "seqPattern" version)) + (sha256 + (base32 + "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq")))) + (properties + `((upstream-name . "seqPattern"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-kernsmooth" ,r-kernsmooth) + ("r-plotrix" ,r-plotrix))) + (home-page "https://bioconductor.org/packages/seqPattern") + (synopsis "Visualising oligonucleotide patterns and motif occurrences") + (description + "This package provides tools to visualize oligonucleotide patterns and +sequence motif occurrences across a large set of sequences centred at a common +reference point and sorted by a user defined feature.") + (license license:gpl3+))) + (define-public r-shortread (package (name "r-shortread") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 566370c37f..fa57451bdc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7976,33 +7976,6 @@ (define-public r-go-db information about the latest version of the Gene Ontologies.") (license license:artistic2.0))) -(define-public r-seqpattern - (package - (name "r-seqpattern") - (version "1.22.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "seqPattern" version)) - (sha256 - (base32 - "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq")))) - (properties - `((upstream-name . "seqPattern"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-plotrix" ,r-plotrix))) - (home-page "https://bioconductor.org/packages/seqPattern") - (synopsis "Visualising oligonucleotide patterns and motif occurrences") - (description - "This package provides tools to visualize oligonucleotide patterns and -sequence motif occurrences across a large set of sequences centred at a common -reference point and sorted by a user defined feature.") - (license license:gpl3+))) - (define-public r-spp (package (name "r-spp") -- cgit v1.2.3 From f3b50aa4fd0c431814c70f02fea62bfcffeebbd4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:43 +0200 Subject: gnu: r-go-db: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-go-db): Move from here... * gnu/packages/bioconductor.scm (r-go-db): ...to here. [source]: Replace 'string-append' by 'bioconductor-uri' with 'annotation. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 24 ------------------------ 2 files changed, 22 insertions(+), 24 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d386f2270e..8cf8b43ed4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -436,6 +436,28 @@ (define-public r-genomeinfodbdata ID and species. It is used by functions in the GenomeInfoDb package.") (license license:artistic2.0))) +(define-public r-go-db + (package + (name "r-go-db") + (version "3.7.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GO.db" version 'annotation)) + (sha256 + (base32 + "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5")))) + (properties + `((upstream-name . "GO.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/GO.db") + (synopsis "Annotation maps describing the entire Gene Ontology") + (description + "The purpose of this GO.db annotation package is to provide detailed +information about the latest version of the Gene Ontologies.") + (license license:artistic2.0))) + (define-public r-homo-sapiens (package (name "r-homo-sapiens") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fa57451bdc..1396631591 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7952,30 +7952,6 @@ (define-public bio-vcf (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-go-db - (package - (name "r-go-db") - (version "3.7.0") - (source (origin - (method url-fetch) - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/GO.db_" - version ".tar.gz")) - (sha256 - (base32 - "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5")))) - (properties - `((upstream-name . "GO.db"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) - (home-page "https://bioconductor.org/packages/GO.db") - (synopsis "Annotation maps describing the entire Gene Ontology") - (description - "The purpose of this GO.db annotation package is to provide detailed -information about the latest version of the Gene Ontologies.") - (license license:artistic2.0))) - (define-public r-spp (package (name "r-spp") -- cgit v1.2.3 From f8fe5497c7b9f598786d46d96fd1bd5002e7e57f Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:44 +0200 Subject: gnu: r-genomation: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-genomation): Move from here... * gnu/packages/bioconductor.scm (r-genomation): ...to here. --- gnu/packages/bioconductor.scm | 48 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 48 ----------------------------------------- 2 files changed, 48 insertions(+), 48 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8cf8b43ed4..b90e315267 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2304,6 +2304,54 @@ (define-public r-genefilter high-throughput sequencing experiments.") (license license:artistic2.0))) +(define-public r-genomation + (package + (name "r-genomation") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "genomation" version)) + (sha256 + (base32 + "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-data-table" ,r-data-table) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-gridbase" ,r-gridbase) + ("r-impute" ,r-impute) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-plotrix" ,r-plotrix) + ("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp) + ("r-readr" ,r-readr) + ("r-reshape2" ,r-reshape2) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-runit" ,r-runit) + ("r-s4vectors" ,r-s4vectors) + ("r-seqpattern" ,r-seqpattern))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioinformatics.mdc-berlin.de/genomation/") + (synopsis "Summary, annotation and visualization of genomic data") + (description + "This package provides a package for summary and annotation of genomic +intervals. Users can visualize and quantify genomic intervals over +pre-defined functional regions, such as promoters, exons, introns, etc. The +genomic intervals represent regions with a defined chromosome position, which +may be associated with a score, such as aligned reads from HT-seq experiments, +TF binding sites, methylation scores, etc. The package can use any tabular +genomic feature data as long as it has minimal information on the locations of +genomic intervals. In addition, it can use BAM or BigWig files as input.") + (license license:artistic2.0))) + (define-public r-genomeinfodb (package (name "r-genomeinfodb") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1396631591..cc6e1b1594 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8023,54 +8023,6 @@ (define-public r-phantompeakqualtools characteristic tag shift values in these assays.") (license license:bsd-3))) -(define-public r-genomation - (package - (name "r-genomation") - (version "1.22.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "genomation" version)) - (sha256 - (base32 - "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-data-table" ,r-data-table) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gridbase" ,r-gridbase) - ("r-impute" ,r-impute) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-plotrix" ,r-plotrix) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-runit" ,r-runit) - ("r-s4vectors" ,r-s4vectors) - ("r-seqpattern" ,r-seqpattern))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioinformatics.mdc-berlin.de/genomation/") - (synopsis "Summary, annotation and visualization of genomic data") - (description - "This package provides a package for summary and annotation of genomic -intervals. Users can visualize and quantify genomic intervals over -pre-defined functional regions, such as promoters, exons, introns, etc. The -genomic intervals represent regions with a defined chromosome position, which -may be associated with a score, such as aligned reads from HT-seq experiments, -TF binding sites, methylation scores, etc. The package can use any tabular -genomic feature data as long as it has minimal information on the locations of -genomic intervals. In addition, it can use BAM or BigWig files as input.") - (license license:artistic2.0))) - (define-public r-genomationdata (package (name "r-genomationdata") -- cgit v1.2.3 From d7fa9c1ffdbd0ab4d4412020c925be39503ce9e8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:45 +0200 Subject: gnu: r-genomationdata: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-genomationdata): Move from here... * gnu/packages/bioconductor.scm (r-genomationdata): ...to here. [source]: Replace 'string-append' by 'bioconductor-uri' with 'experiment. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 28 ---------------------------- 2 files changed, 26 insertions(+), 28 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b90e315267..b25cc8e019 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1170,6 +1170,32 @@ (define-public r-geneoverlap and visualize the results.") (license license:gpl3))) +(define-public r-genomationdata + (package + (name "r-genomationdata") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "genomationData" version 'experiment)) + (sha256 + (base32 + "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g")))) + (properties + `((upstream-name . "genomationData"))) + (build-system r-build-system) + ;; As this package provides little more than large data files, it doesn't + ;; make sense to build substitutes. + (arguments `(#:substitutable? #f)) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioinformatics.mdc-berlin.de/genomation/") + (synopsis "Experimental data for use with the genomation package") + (description + "This package contains experimental genetic data for use with the +genomation package. Included are Chip Seq, Methylation and Cage data, +downloaded from Encode.") + (license license:gpl3+))) + (define-public r-pasilla (package (name "r-pasilla") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cc6e1b1594..1b94b62b1d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8023,34 +8023,6 @@ (define-public r-phantompeakqualtools characteristic tag shift values in these assays.") (license license:bsd-3))) -(define-public r-genomationdata - (package - (name "r-genomationdata") - (version "1.22.0") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://bioconductor.org/packages/" - "release/data/experiment/src/contrib/" - "genomationData_" version ".tar.gz")) - (sha256 - (base32 - "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g")))) - (build-system r-build-system) - ;; As this package provides little more than large data files, it doesn't - ;; make sense to build substitutes. - (arguments `(#:substitutable? #f)) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioinformatics.mdc-berlin.de/genomation/") - (synopsis "Experimental data for use with the genomation package") - (description - "This package contains experimental genetic data for use with the -genomation package. Included are Chip Seq, Methylation and Cage data, -downloaded from Encode.") - (license license:gpl3+))) - (define-public r-seqlogo (package (name "r-seqlogo") -- cgit v1.2.3 From ad46c8aa7f8ae74aa8f594b4cd663ea2ea9a8115 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:46 +0200 Subject: gnu: r-pcamethods: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-pcamethods): Move from here... * gnu/packages/bioconductor.scm (r-pcamethods): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b25cc8e019..e70f2bc13d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2731,6 +2731,36 @@ (define-public r-msnid and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) +(define-public r-pcamethods + (package + (name "r-pcamethods") + (version "1.82.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "pcaMethods" version)) + (sha256 + (base32 + "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0")))) + (properties `((upstream-name . "pcaMethods"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/hredestig/pcamethods") + (synopsis "Collection of PCA methods") + (description + "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, +Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method +for missing value estimation is included for comparison. BPCA, PPCA and +NipalsPCA may be used to perform PCA on incomplete data as well as for +accurate missing value estimation. A set of methods for printing and plotting +the results is also provided. All PCA methods make use of the same data +structure (pcaRes) to provide a common interface to the PCA results.") + (license license:gpl3+))) + (define-public r-rbgl (package (name "r-rbgl") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1b94b62b1d..a2c99ecbd6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9227,36 +9227,6 @@ (define-public r-mzid specific parser.") (license license:gpl2+))) -(define-public r-pcamethods - (package - (name "r-pcamethods") - (version "1.82.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "pcaMethods" version)) - (sha256 - (base32 - "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0")))) - (properties `((upstream-name . "pcaMethods"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp))) - (home-page "https://github.com/hredestig/pcamethods") - (synopsis "Collection of PCA methods") - (description - "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, -Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method -for missing value estimation is included for comparison. BPCA, PPCA and -NipalsPCA may be used to perform PCA on incomplete data as well as for -accurate missing value estimation. A set of methods for printing and plotting -the results is also provided. All PCA methods make use of the same data -structure (pcaRes) to provide a common interface to the PCA results.") - (license license:gpl3+))) - (define-public r-aroma-light (package (name "r-aroma-light") -- cgit v1.2.3 From 7756e08b44b40ff46357572befa81fb173ca7edc Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:47 +0200 Subject: gnu: r-mzid: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-mzid): Move from here... * gnu/packages/bioconductor.scm (r-mzid): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e70f2bc13d..8fc035b623 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2731,6 +2731,37 @@ (define-public r-msnid and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) +(define-public r-mzid + (package + (name "r-mzid") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mzID" version)) + (sha256 + (base32 + "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2")))) + (properties `((upstream-name . "mzID"))) + (build-system r-build-system) + (propagated-inputs + `(("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) + ("r-iterators" ,r-iterators) + ("r-plyr" ,r-plyr) + ("r-protgenerics" ,r-protgenerics) + ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/mzID") + (synopsis "Parser for mzIdentML files") + (description + "This package provides a parser for mzIdentML files implemented using the +XML package. The parser tries to be general and able to handle all types of +mzIdentML files with the drawback of having less pretty output than a vendor +specific parser.") + (license license:gpl2+))) + (define-public r-pcamethods (package (name "r-pcamethods") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a2c99ecbd6..f6ec7e32c4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9196,37 +9196,6 @@ (define-public r-vsn and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-mzid - (package - (name "r-mzid") - (version "1.28.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "mzID" version)) - (sha256 - (base32 - "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2")))) - (properties `((upstream-name . "mzID"))) - (build-system r-build-system) - (propagated-inputs - `(("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-iterators" ,r-iterators) - ("r-plyr" ,r-plyr) - ("r-protgenerics" ,r-protgenerics) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/mzID") - (synopsis "Parser for mzIdentML files") - (description - "This package provides a parser for mzIdentML files implemented using the -XML package. The parser tries to be general and able to handle all types of -mzIdentML files with the drawback of having less pretty output than a vendor -specific parser.") - (license license:gpl2+))) - (define-public r-aroma-light (package (name "r-aroma-light") -- cgit v1.2.3 From bb118f20fe6581a4acbd3799ed31ab0d21e72e78 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:48 +0200 Subject: gnu: r-aroma-light: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-aroma-light): Move from here... * gnu/packages/bioconductor.scm (r-aroma-light): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8fc035b623..3f057a3a4d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1987,6 +1987,33 @@ (define-public r-annotationforge databases. Packages produced are intended to be used with AnnotationDbi.") (license license:artistic2.0))) +(define-public r-aroma-light + (package + (name "r-aroma-light") + (version "3.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "aroma.light" version)) + (sha256 + (base32 + "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0")))) + (properties `((upstream-name . "aroma.light"))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrixstats" ,r-matrixstats) + ("r-r-methodss3" ,r-r-methodss3) + ("r-r-oo" ,r-r-oo) + ("r-r-utils" ,r-r-utils))) + (home-page "https://github.com/HenrikBengtsson/aroma.light") + (synopsis "Methods for normalization and visualization of microarray data") + (description + "This package provides methods for microarray analysis that take basic +data types such as matrices and lists of vectors. These methods can be used +standalone, be utilized in other packages, or be wrapped up in higher-level +classes.") + (license license:gpl2+))) + (define-public r-biobase (package (name "r-biobase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f6ec7e32c4..687da8086e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9196,33 +9196,6 @@ (define-public r-vsn and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-aroma-light - (package - (name "r-aroma-light") - (version "3.20.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "aroma.light" version)) - (sha256 - (base32 - "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0")))) - (properties `((upstream-name . "aroma.light"))) - (build-system r-build-system) - (propagated-inputs - `(("r-matrixstats" ,r-matrixstats) - ("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo) - ("r-r-utils" ,r-r-utils))) - (home-page "https://github.com/HenrikBengtsson/aroma.light") - (synopsis "Methods for normalization and visualization of microarray data") - (description - "This package provides methods for microarray analysis that take basic -data types such as matrices and lists of vectors. These methods can be used -standalone, be utilized in other packages, or be wrapped up in higher-level -classes.") - (license license:gpl2+))) - (define-public r-deseq (package (name "r-deseq") -- cgit v1.2.3 From ef954bb4884185466bc4833c365ecb01be3a0a20 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:49 +0200 Subject: gnu: r-deseq: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-deseq): Move from here... * gnu/packages/bioconductor.scm (r-deseq): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3f057a3a4d..65dfce04bd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2218,6 +2218,37 @@ (define-public r-category analysis.") (license license:artistic2.0))) +(define-public r-deseq + (package + (name "r-deseq") + (version "1.39.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DESeq" version)) + (sha256 + (base32 + "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1")))) + (properties `((upstream-name . "DESeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genefilter" ,r-genefilter) + ("r-geneplotter" ,r-geneplotter) + ("r-lattice" ,r-lattice) + ("r-locfit" ,r-locfit) + ("r-mass" ,r-mass) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "https://www-huber.embl.de/users/anders/DESeq/") + (synopsis "Differential gene expression analysis") + (description + "This package provides tools for estimating variance-mean dependence in +count data from high-throughput genetic sequencing assays and for testing for +differential expression based on a model using the negative binomial +distribution.") + (license license:gpl3+))) + (define-public r-deseq2 (package (name "r-deseq2") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 687da8086e..d23c3cb94e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9196,37 +9196,6 @@ (define-public r-vsn and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-deseq - (package - (name "r-deseq") - (version "1.39.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DESeq" version)) - (sha256 - (base32 - "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1")))) - (properties `((upstream-name . "DESeq"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-lattice" ,r-lattice) - ("r-locfit" ,r-locfit) - ("r-mass" ,r-mass) - ("r-rcolorbrewer" ,r-rcolorbrewer))) - (home-page "https://www-huber.embl.de/users/anders/DESeq/") - (synopsis "Differential gene expression analysis") - (description - "This package provides tools for estimating variance-mean dependence in -count data from high-throughput genetic sequencing assays and for testing for -differential expression based on a model using the negative binomial -distribution.") - (license license:gpl3+))) - (define-public r-edaseq (package (name "r-edaseq") -- cgit v1.2.3 From f6f43a2d40e830243d118f740d164d3fe1b79bba Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:50 +0200 Subject: gnu: r-edaseq: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-edaseq): Move from here... * gnu/packages/bioconductor.scm (r-edaseq): ...to here. --- gnu/packages/bioconductor.scm | 40 ++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 40 ---------------------------------------- 2 files changed, 40 insertions(+), 40 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 65dfce04bd..7e6b48eb19 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2332,6 +2332,46 @@ (define-public r-dexseq exploration of the results.") (license license:gpl3+))) +(define-public r-edaseq + (package + (name "r-edaseq") + (version "2.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EDASeq" version)) + (sha256 + (base32 + "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip")))) + (properties `((upstream-name . "EDASeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-aroma-light" ,r-aroma-light) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-shortread" ,r-shortread))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/drisso/EDASeq") + (synopsis "Exploratory data analysis and normalization for RNA-Seq") + (description + "This package provides support for numerical and graphical summaries of +RNA-Seq genomic read data. Provided within-lane normalization procedures to +adjust for GC-content effect (or other gene-level effects) on read counts: +loess robust local regression, global-scaling, and full-quantile +normalization. Between-lane normalization procedures to adjust for +distributional differences between lanes (e.g., sequencing depth): +global-scaling and full-quantile normalization.") + (license license:artistic2.0))) + (define-public r-edger (package (name "r-edger") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d23c3cb94e..87ba47e2e4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9196,46 +9196,6 @@ (define-public r-vsn and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-edaseq - (package - (name "r-edaseq") - (version "2.24.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "EDASeq" version)) - (sha256 - (base32 - "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip")))) - (properties `((upstream-name . "EDASeq"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-aroma-light" ,r-aroma-light) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-shortread" ,r-shortread))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/drisso/EDASeq") - (synopsis "Exploratory data analysis and normalization for RNA-Seq") - (description - "This package provides support for numerical and graphical summaries of -RNA-Seq genomic read data. Provided within-lane normalization procedures to -adjust for GC-content effect (or other gene-level effects) on read counts: -loess robust local regression, global-scaling, and full-quantile -normalization. Between-lane normalization procedures to adjust for -distributional differences between lanes (e.g., sequencing depth): -global-scaling and full-quantile normalization.") - (license license:artistic2.0))) - (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") -- cgit v1.2.3 From dfe6224f5f42993eb8bcf2659d6da99f8c7fd1ac Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:51 +0200 Subject: gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Move from here... * gnu/packages/bioconductor.scm (r-interactivedisplaybase): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7e6b48eb19..53f1005d7b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2713,6 +2713,33 @@ (define-public r-impute microarray data, using nearest neighbor averaging.") (license license:gpl2+))) +(define-public r-interactivedisplaybase + (package + (name "r-interactivedisplaybase") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "interactiveDisplayBase" version)) + (sha256 + (base32 + "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01")))) + (properties + `((upstream-name . "interactiveDisplayBase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-dt" ,r-dt) + ("r-shiny" ,r-shiny))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/interactiveDisplayBase") + (synopsis "Base package for web displays of Bioconductor objects") + (description + "This package contains the basic methods needed to generate interactive +Shiny-based display methods for Bioconductor objects.") + (license license:artistic2.0))) + (define-public r-limma (package (name "r-limma") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 87ba47e2e4..38286fb974 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9196,33 +9196,6 @@ (define-public r-vsn and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-interactivedisplaybase - (package - (name "r-interactivedisplaybase") - (version "1.28.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "interactiveDisplayBase" version)) - (sha256 - (base32 - "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01")))) - (properties - `((upstream-name . "interactiveDisplayBase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-dt" ,r-dt) - ("r-shiny" ,r-shiny))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/interactiveDisplayBase") - (synopsis "Base package for web displays of Bioconductor objects") - (description - "This package contains the basic methods needed to generate interactive -Shiny-based display methods for Bioconductor objects.") - (license license:artistic2.0))) - (define-public r-annotationhub (package (name "r-annotationhub") -- cgit v1.2.3 From 9644745692aa2407e66f2ce4671356c3231c462d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:52 +0200 Subject: gnu: r-annotationhub: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-annotationhub): Move from here... * gnu/packages/bioconductor.scm (r-annotationhub): ...to here. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 41 ----------------------------------------- 2 files changed, 41 insertions(+), 41 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 53f1005d7b..42a01a4dc3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1987,6 +1987,47 @@ (define-public r-annotationforge databases. Packages produced are intended to be used with AnnotationDbi.") (license license:artistic2.0))) +(define-public r-annotationhub + (package + (name "r-annotationhub") + (version "2.22.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationHub" version)) + (sha256 + (base32 + "08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5")))) + (properties `((upstream-name . "AnnotationHub"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocfilecache" ,r-biocfilecache) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-biocversion" ,r-biocversion) + ("r-curl" ,r-curl) + ("r-dplyr" ,r-dplyr) + ("r-httr" ,r-httr) + ("r-interactivedisplaybase" ,r-interactivedisplaybase) + ("r-rappdirs" ,r-rappdirs) + ("r-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors) + ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/AnnotationHub") + (synopsis "Client to access AnnotationHub resources") + (description + "This package provides a client for the Bioconductor AnnotationHub web +resource. The AnnotationHub web resource provides a central location where +genomic files (e.g. VCF, bed, wig) and other resources from standard +locations (e.g. UCSC, Ensembl) can be discovered. The resource includes +metadata about each resource, e.g., a textual description, tags, and date of +modification. The client creates and manages a local cache of files retrieved +by the user, helping with quick and reproducible access.") + (license license:artistic2.0))) + (define-public r-aroma-light (package (name "r-aroma-light") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 38286fb974..104a37acaa 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9196,47 +9196,6 @@ (define-public r-vsn and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-annotationhub - (package - (name "r-annotationhub") - (version "2.22.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "AnnotationHub" version)) - (sha256 - (base32 - "08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5")))) - (properties `((upstream-name . "AnnotationHub"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biocversion" ,r-biocversion) - ("r-curl" ,r-curl) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-interactivedisplaybase" ,r-interactivedisplaybase) - ("r-rappdirs" ,r-rappdirs) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/AnnotationHub") - (synopsis "Client to access AnnotationHub resources") - (description - "This package provides a client for the Bioconductor AnnotationHub web -resource. The AnnotationHub web resource provides a central location where -genomic files (e.g. VCF, bed, wig) and other resources from standard -locations (e.g. UCSC, Ensembl) can be discovered. The resource includes -metadata about each resource, e.g., a textual description, tags, and date of -modification. The client creates and manages a local cache of files retrieved -by the user, helping with quick and reproducible access.") - (license license:artistic2.0))) - (define-public r-fastseg (package (name "r-fastseg") -- cgit v1.2.3 From 32ae36e96f9b076901af94c723e3d156595d5bc5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:53 +0200 Subject: gnu: r-fastseg: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-fastseg): Move from here... * gnu/packages/bioconductor.scm (r-fastseg): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 42a01a4dc3..07ce719d7d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2441,6 +2441,36 @@ (define-public r-edger CAGE.") (license license:gpl2+))) +(define-public r-fastseg + (package + (name "r-fastseg") + (version "1.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "fastseg" version)) + (sha256 + (base32 + "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://www.bioinf.jku.at/software/fastseg/index.html") + (synopsis "Fast segmentation algorithm for genetic sequencing data") + (description + "Fastseg implements a very fast and efficient segmentation algorithm. +It can segment data from DNA microarrays and data from next generation +sequencing for example to detect copy number segments. Further it can segment +data from RNA microarrays like tiling arrays to identify transcripts. Most +generally, it can segment data given as a matrix or as a vector. Various data +formats can be used as input to fastseg like expression set objects for +microarrays or GRanges for sequencing data.") + (license license:lgpl2.0+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 104a37acaa..54c3945489 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9196,36 +9196,6 @@ (define-public r-vsn and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-fastseg - (package - (name "r-fastseg") - (version "1.36.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "fastseg" version)) - (sha256 - (base32 - "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://www.bioinf.jku.at/software/fastseg/index.html") - (synopsis "Fast segmentation algorithm for genetic sequencing data") - (description - "Fastseg implements a very fast and efficient segmentation algorithm. -It can segment data from DNA microarrays and data from next generation -sequencing for example to detect copy number segments. Further it can segment -data from RNA microarrays like tiling arrays to identify transcripts. Most -generally, it can segment data given as a matrix or as a vector. Various data -formats can be used as input to fastseg like expression set objects for -microarrays or GRanges for sequencing data.") - (license license:lgpl2.0+))) - (define-public r-keggrest (package (name "r-keggrest") -- cgit v1.2.3 From 22cda2e4320a59a4c26fbbbadf4064526d2b2c82 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:54 +0200 Subject: gnu: r-affy: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-affy): Move from here... * gnu/packages/bioconductor.scm (r-affy): ...to here. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 28 ---------------------------- 2 files changed, 28 insertions(+), 28 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 07ce719d7d..25094e771e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1755,6 +1755,34 @@ (define-public r-nmf performing parallel computations on multicore machines.") (license license:gpl2+))) +(define-public r-affy + (package + (name "r-affy") + (version "1.68.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affy" version)) + (sha256 + (base32 + "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06")))) + (build-system r-build-system) + (propagated-inputs + `(("r-affyio" ,r-affyio) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-preprocesscore" ,r-preprocesscore) + ("r-zlibbioc" ,r-zlibbioc))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://bioconductor.org/packages/affy") + (synopsis "Methods for affymetrix oligonucleotide arrays") + (description + "This package contains functions for exploratory oligonucleotide array +analysis.") + (license license:lgpl2.0+))) + (define-public r-affycomp (package (name "r-affycomp") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 54c3945489..df0d4e73c1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9132,34 +9132,6 @@ (define-public r-affyio CDF file formats.") (license license:lgpl2.0+))) -(define-public r-affy - (package - (name "r-affy") - (version "1.68.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "affy" version)) - (sha256 - (base32 - "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06")))) - (build-system r-build-system) - (propagated-inputs - `(("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-preprocesscore" ,r-preprocesscore) - ("r-zlibbioc" ,r-zlibbioc))) - (inputs - `(("zlib" ,zlib))) - (home-page "https://bioconductor.org/packages/affy") - (synopsis "Methods for affymetrix oligonucleotide arrays") - (description - "This package contains functions for exploratory oligonucleotide array -analysis.") - (license license:lgpl2.0+))) - (define-public r-vsn (package (name "r-vsn") -- cgit v1.2.3 From d0a5503752cab62efbaa06bd00fb92145e015732 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:55 +0200 Subject: gnu: r-keggrest: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-keggrest): Move from here... * gnu/packages/bioconductor.scm (r-keggrest): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 25094e771e..28e8810bbc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2839,6 +2839,32 @@ (define-public r-interactivedisplaybase Shiny-based display methods for Bioconductor objects.") (license license:artistic2.0))) +(define-public r-keggrest + (package + (name "r-keggrest") + (version "1.30.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "KEGGREST" version)) + (sha256 + (base32 + "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s")))) + (properties `((upstream-name . "KEGGREST"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-httr" ,r-httr) + ("r-png" ,r-png))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/KEGGREST") + (synopsis "Client-side REST access to KEGG") + (description + "This package provides a package that provides a client interface to the +@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.") + (license license:artistic2.0))) + (define-public r-limma (package (name "r-limma") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index df0d4e73c1..8188b50ad6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9168,32 +9168,6 @@ (define-public r-vsn and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-keggrest - (package - (name "r-keggrest") - (version "1.30.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "KEGGREST" version)) - (sha256 - (base32 - "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s")))) - (properties `((upstream-name . "KEGGREST"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-httr" ,r-httr) - ("r-png" ,r-png))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/KEGGREST") - (synopsis "Client-side REST access to KEGG") - (description - "This package provides a package that provides a client interface to the -@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.") - (license license:artistic2.0))) - (define-public r-gage (package (name "r-gage") -- cgit v1.2.3 From 84019edf38fea7ded047464fa4a6c79675934ae4 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:56 +0200 Subject: gnu: r-gage: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-gage): Move from here... * gnu/packages/bioconductor.scm (r-gage): ...to here. --- gnu/packages/bioconductor.scm | 33 ++++++++++++++++++++++++++++++++- gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 32 insertions(+), 32 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 28e8810bbc..a0ee8a8c18 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017 Efraim Flashner -;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu @@ -2499,6 +2499,37 @@ (define-public r-fastseg microarrays or GRanges for sequencing data.") (license license:lgpl2.0+))) +(define-public r-gage + (package + (name "r-gage") + (version "2.40.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gage" version)) + (sha256 + (base32 + "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-go-db" ,r-go-db) + ("r-graph" ,r-graph) + ("r-keggrest" ,r-keggrest))) + (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" + "articles/10.1186/1471-2105-10-161")) + (synopsis "Generally applicable gene-set enrichment for pathway analysis") + (description + "GAGE is a published method for gene set (enrichment or GSEA) or pathway +analysis. GAGE is generally applicable independent of microarray or RNA-Seq +data attributes including sample sizes, experimental designs, assay platforms, +and other types of heterogeneity. The gage package provides functions for +basic GAGE analysis, result processing and presentation. In addition, it +provides demo microarray data and commonly used gene set data based on KEGG +pathways and GO terms. These functions and data are also useful for gene set +analysis using other methods.") + (license license:gpl2+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8188b50ad6..a857c1ccc5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9168,37 +9168,6 @@ (define-public r-vsn and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-gage - (package - (name "r-gage") - (version "2.40.2") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "gage" version)) - (sha256 - (base32 - "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-keggrest" ,r-keggrest))) - (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" - "articles/10.1186/1471-2105-10-161")) - (synopsis "Generally applicable gene-set enrichment for pathway analysis") - (description - "GAGE is a published method for gene set (enrichment or GSEA) or pathway -analysis. GAGE is generally applicable independent of microarray or RNA-Seq -data attributes including sample sizes, experimental designs, assay platforms, -and other types of heterogeneity. The gage package provides functions for -basic GAGE analysis, result processing and presentation. In addition, it -provides demo microarray data and commonly used gene set data based on KEGG -pathways and GO terms. These functions and data are also useful for gene set -analysis using other methods.") - (license license:gpl2+))) - (define-public r-genomicfiles (package (name "r-genomicfiles") -- cgit v1.2.3 From ff65fa90d268bbe3f868be4cb5d9e2bb5ab6c3dd Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:57 +0200 Subject: gnu: r-complexheatmap: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-complexheatmap): Move from here... * gnu/packages/bioconductor.scm (r-complexheatmap): ...to here. --- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 39 --------------------------------------- 2 files changed, 39 insertions(+), 39 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a0ee8a8c18..3e536e0299 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2287,6 +2287,45 @@ (define-public r-category analysis.") (license license:artistic2.0))) +(define-public r-complexheatmap + (package + (name "r-complexheatmap") + (version "2.6.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ComplexHeatmap" version)) + (sha256 + (base32 + "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x")))) + (properties + `((upstream-name . "ComplexHeatmap"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cairo" ,r-cairo) + ("r-circlize" ,r-circlize) + ("r-clue" ,r-clue) + ("r-colorspace" ,r-colorspace) + ("r-digest" ,r-digest) + ("r-getoptlong" ,r-getoptlong) + ("r-globaloptions" ,r-globaloptions) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-png" ,r-png) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page + "https://github.com/jokergoo/ComplexHeatmap") + (synopsis "Making Complex Heatmaps") + (description + "Complex heatmaps are efficient to visualize associations between +different sources of data sets and reveal potential structures. This package +provides a highly flexible way to arrange multiple heatmaps and supports +self-defined annotation graphics.") + (license license:gpl2+))) + (define-public r-deseq (package (name "r-deseq") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a857c1ccc5..a57c420a07 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9202,45 +9202,6 @@ (define-public r-genomicfiles provide added flexibility for data combination and manipulation.") (license license:artistic2.0))) -(define-public r-complexheatmap - (package - (name "r-complexheatmap") - (version "2.6.2") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ComplexHeatmap" version)) - (sha256 - (base32 - "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x")))) - (properties - `((upstream-name . "ComplexHeatmap"))) - (build-system r-build-system) - (propagated-inputs - `(("r-cairo" ,r-cairo) - ("r-circlize" ,r-circlize) - ("r-clue" ,r-clue) - ("r-colorspace" ,r-colorspace) - ("r-digest" ,r-digest) - ("r-getoptlong" ,r-getoptlong) - ("r-globaloptions" ,r-globaloptions) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page - "https://github.com/jokergoo/ComplexHeatmap") - (synopsis "Making Complex Heatmaps") - (description - "Complex heatmaps are efficient to visualize associations between -different sources of data sets and reveal potential structures. This package -provides a highly flexible way to arrange multiple heatmaps and supports -self-defined annotation graphics.") - (license license:gpl2+))) - (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") -- cgit v1.2.3 From 0b5b41c5614be969e611f3dc3e1462eb8135b3e8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:58 +0200 Subject: gnu: r-genomicfiles: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-genomicfiles): Move from here... * gnu/packages/bioconductor.scm (r-genomicfiles): ...to here. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 34 ---------------------------------- 2 files changed, 34 insertions(+), 34 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3e536e0299..c369ac0cb4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2751,6 +2751,40 @@ (define-public r-genomicfeatures extracting the desired features in a convenient format.") (license license:artistic2.0))) +(define-public r-genomicfiles + (package + (name "r-genomicfiles") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicFiles" version)) + (sha256 + (base32 + "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz")))) + (properties `((upstream-name . "GenomicFiles"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrixgenerics" ,r-matrixgenerics) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/GenomicFiles") + (synopsis "Distributed computing by file or by range") + (description + "This package provides infrastructure for parallel computations +distributed by file or by range. User defined mapper and reducer functions +provide added flexibility for data combination and manipulation.") + (license license:artistic2.0))) + (define-public r-genomicranges (package (name "r-genomicranges") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a57c420a07..38f3298c23 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9168,40 +9168,6 @@ (define-public r-vsn and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-genomicfiles - (package - (name "r-genomicfiles") - (version "1.26.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicFiles" version)) - (sha256 - (base32 - "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz")))) - (properties `((upstream-name . "GenomicFiles"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (home-page "https://bioconductor.org/packages/GenomicFiles") - (synopsis "Distributed computing by file or by range") - (description - "This package provides infrastructure for parallel computations -distributed by file or by range. User defined mapper and reducer functions -provide added flexibility for data combination and manipulation.") - (license license:artistic2.0))) - (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") -- cgit v1.2.3 From d1ea2b7c8b76dea810102379112b05d344b02530 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:25:59 +0200 Subject: gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Move from here... * gnu/packages/bioconductor.scm (r-dirichletmultinomial): ...to here. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c369ac0cb4..fea0fe78ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2440,6 +2440,35 @@ (define-public r-dexseq exploration of the results.") (license license:gpl3+))) +(define-public r-dirichletmultinomial + (package + (name "r-dirichletmultinomial") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DirichletMultinomial" version)) + (sha256 + (base32 + "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk")))) + (properties + `((upstream-name . "DirichletMultinomial"))) + (build-system r-build-system) + (inputs + `(("gsl" ,gsl))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/DirichletMultinomial") + (synopsis "Dirichlet-Multinomial mixture models for microbiome data") + (description + "Dirichlet-multinomial mixture models can be used to describe variability +in microbial metagenomic data. This package is an interface to code +originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): +1-15.") + (license license:lgpl3))) + (define-public r-edaseq (package (name "r-edaseq") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 38f3298c23..dd095b6e05 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9168,35 +9168,6 @@ (define-public r-vsn and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-dirichletmultinomial - (package - (name "r-dirichletmultinomial") - (version "1.32.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DirichletMultinomial" version)) - (sha256 - (base32 - "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk")))) - (properties - `((upstream-name . "DirichletMultinomial"))) - (build-system r-build-system) - (inputs - `(("gsl" ,gsl))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/DirichletMultinomial") - (synopsis "Dirichlet-Multinomial mixture models for microbiome data") - (description - "Dirichlet-multinomial mixture models can be used to describe variability -in microbial metagenomic data. This package is an interface to code -originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): -1-15.") - (license license:lgpl3))) - (define-public r-ensembldb (package (name "r-ensembldb") -- cgit v1.2.3 From 8182e6a6fd10bc6e8fb04a4a95df19266aa0b6b2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:00 +0200 Subject: gnu: r-organismdbi: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-organismdbi): Move from here... * gnu/packages/bioconductor.scm (r-organismdbi): ...to here. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 32 -------------------------------- 2 files changed, 32 insertions(+), 32 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fea0fe78ac..659c8f5c82 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3145,6 +3145,38 @@ (define-public r-mzid specific parser.") (license license:gpl2+))) +(define-public r-organismdbi + (package + (name "r-organismdbi") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "OrganismDbi" version)) + (sha256 + (base32 + "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw")))) + (properties `((upstream-name . "OrganismDbi"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-dbi" ,r-dbi) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-graph" ,r-graph) + ("r-iranges" ,r-iranges) + ("r-rbgl" ,r-rbgl) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/OrganismDbi") + (synopsis "Software to enable the smooth interfacing of database packages") + (description "The package enables a simple unified interface to several +annotation packages each of which has its own schema by taking advantage of +the fact that each of these packages implements a select methods.") + (license license:artistic2.0))) + (define-public r-pcamethods (package (name "r-pcamethods") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dd095b6e05..9e7bae2525 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9213,38 +9213,6 @@ (define-public r-ensembldb ;; No version specified (license license:lgpl3+))) -(define-public r-organismdbi - (package - (name "r-organismdbi") - (version "1.32.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "OrganismDbi" version)) - (sha256 - (base32 - "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw")))) - (properties `((upstream-name . "OrganismDbi"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-dbi" ,r-dbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-graph" ,r-graph) - ("r-iranges" ,r-iranges) - ("r-rbgl" ,r-rbgl) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/OrganismDbi") - (synopsis "Software to enable the smooth interfacing of database packages") - (description "The package enables a simple unified interface to several -annotation packages each of which has its own schema by taking advantage of -the fact that each of these packages implements a select methods.") - (license license:artistic2.0))) - (define-public r-biovizbase (package (name "r-biovizbase") -- cgit v1.2.3 From 96ae9822c4c641587ea151e6a58eddbdb6e66590 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:01 +0200 Subject: gnu: r-affyio: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-affyio): Move from here... * gnu/packages/bioconductor.scm (r-affyio): ...to here. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 24 ------------------------ 2 files changed, 24 insertions(+), 24 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 659c8f5c82..9faf7021da 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1899,6 +1899,30 @@ (define-public r-affycoretools to streamline the more common analyses that a Biostatistician might see.") (license license:artistic2.0))) +(define-public r-affyio + (package + (name "r-affyio") + (version "1.60.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affyio" version)) + (sha256 + (base32 + "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h")))) + (build-system r-build-system) + (propagated-inputs + `(("r-zlibbioc" ,r-zlibbioc))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/bmbolstad/affyio") + (synopsis "Tools for parsing Affymetrix data files") + (description + "This package provides routines for parsing Affymetrix data files based +upon file format information. The primary focus is on accessing the CEL and +CDF file formats.") + (license license:lgpl2.0+))) + (define-public r-affxparser (package (name "r-affxparser") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9e7bae2525..0dd362c8ee 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9108,30 +9108,6 @@ (define-public r-mzr previously been used in XCMS.") (license license:artistic2.0))) -(define-public r-affyio - (package - (name "r-affyio") - (version "1.60.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "affyio" version)) - (sha256 - (base32 - "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h")))) - (build-system r-build-system) - (propagated-inputs - `(("r-zlibbioc" ,r-zlibbioc))) - (inputs - `(("zlib" ,zlib))) - (home-page "https://github.com/bmbolstad/affyio") - (synopsis "Tools for parsing Affymetrix data files") - (description - "This package provides routines for parsing Affymetrix data files based -upon file format information. The primary focus is on accessing the CEL and -CDF file formats.") - (license license:lgpl2.0+))) - (define-public r-vsn (package (name "r-vsn") -- cgit v1.2.3 From 8d4311bb8e0e7ae68f0182bf232f598ebe2835e5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:02 +0200 Subject: gnu: r-vsn: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-vsn): Move from here... * gnu/packages/bioconductor.scm (r-vsn): ...to here. --- gnu/packages/bioconductor.scm | 36 ++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 36 ------------------------------------ 2 files changed, 36 insertions(+), 36 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9faf7021da..a631143102 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3746,6 +3746,42 @@ (define-public r-variantannotation coding changes and predict coding outcomes.") (license license:artistic2.0))) +(define-public r-vsn + (package + (name "r-vsn") + (version "3.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "vsn" version)) + (sha256 + (base32 + "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-ggplot2" ,r-ggplot2) + ("r-lattice" ,r-lattice) + ("r-limma" ,r-limma))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") + (synopsis "Variance stabilization and calibration for microarray data") + (description + "The package implements a method for normalising microarray intensities, +and works for single- and multiple-color arrays. It can also be used for data +from other technologies, as long as they have similar format. The method uses +a robust variant of the maximum-likelihood estimator for an +additive-multiplicative error model and affine calibration. The model +incorporates data calibration step (a.k.a. normalization), a model for the +dependence of the variance on the mean intensity and a variance stabilizing +data transformation. Differences between transformed intensities are +analogous to \"normalized log-ratios\". However, in contrast to the latter, +their variance is independent of the mean, and they are usually more sensitive +and specific in detecting differential transcription.") + (license license:artistic2.0))) + (define-public r-xvector (package (name "r-xvector") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0dd362c8ee..d133764963 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9108,42 +9108,6 @@ (define-public r-mzr previously been used in XCMS.") (license license:artistic2.0))) -(define-public r-vsn - (package - (name "r-vsn") - (version "3.58.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "vsn" version)) - (sha256 - (base32 - "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb")))) - (build-system r-build-system) - (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-ggplot2" ,r-ggplot2) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma))) - (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes - (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") - (synopsis "Variance stabilization and calibration for microarray data") - (description - "The package implements a method for normalising microarray intensities, -and works for single- and multiple-color arrays. It can also be used for data -from other technologies, as long as they have similar format. The method uses -a robust variant of the maximum-likelihood estimator for an -additive-multiplicative error model and affine calibration. The model -incorporates data calibration step (a.k.a. normalization), a model for the -dependence of the variance on the mean intensity and a variance stabilizing -data transformation. Differences between transformed intensities are -analogous to \"normalized log-ratios\". However, in contrast to the latter, -their variance is independent of the mean, and they are usually more sensitive -and specific in detecting differential transcription.") - (license license:artistic2.0))) - (define-public r-ensembldb (package (name "r-ensembldb") -- cgit v1.2.3 From fea33b9d1e35c18fb214c12653b7624a627271d9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:03 +0200 Subject: gnu: r-biovizbase: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-biovizbase): Move from here... * gnu/packages/bioconductor.scm (r-biovizbase): ...to here. --- gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 42 ----------------------------------------- 2 files changed, 42 insertions(+), 42 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a631143102..56e7186209 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2249,6 +2249,48 @@ (define-public r-biostrings biological sequences or sets of sequences.") (license license:artistic2.0))) +(define-public r-biovizbase + (package + (name "r-biovizbase") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biovizBase" version)) + (sha256 + (base32 + "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq")))) + (properties `((upstream-name . "biovizBase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-dichromat" ,r-dichromat) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-hmisc" ,r-hmisc) + ("r-iranges" ,r-iranges) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rlang" ,r-rlang) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/biovizBase") + (synopsis "Basic graphic utilities for visualization of genomic data") + (description + "The biovizBase package is designed to provide a set of utilities, color +schemes and conventions for genomic data. It serves as the base for various +high-level packages for biological data visualization. This saves development +effort and encourages consistency.") + (license license:artistic2.0))) + (define-public r-bsgenome (package (name "r-bsgenome") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d133764963..b17ca0fabd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9153,48 +9153,6 @@ (define-public r-ensembldb ;; No version specified (license license:lgpl3+))) -(define-public r-biovizbase - (package - (name "r-biovizbase") - (version "1.38.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "biovizBase" version)) - (sha256 - (base32 - "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq")))) - (properties `((upstream-name . "biovizBase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dichromat" ,r-dichromat) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (home-page "https://bioconductor.org/packages/biovizBase") - (synopsis "Basic graphic utilities for visualization of genomic data") - (description - "The biovizBase package is designed to provide a set of utilities, color -schemes and conventions for genomic data. It serves as the base for various -high-level packages for biological data visualization. This saves development -effort and encourages consistency.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit v1.2.3 From 88cf24febb43768c780d55cd496034d227096550 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:04 +0200 Subject: gnu: r-ensembldb: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-ensembldb): Move from here... * gnu/packages/bioconductor.scm (r-ensembldb): ...to here. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 45 ----------------------------------------- 2 files changed, 45 insertions(+), 45 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 56e7186209..eb0bcb22c6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2603,6 +2603,51 @@ (define-public r-edger CAGE.") (license license:gpl2+))) +(define-public r-ensembldb + (package + (name "r-ensembldb") + (version "2.14.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ensembldb" version)) + (sha256 + (base32 + "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-curl" ,r-curl) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-protgenerics" ,r-protgenerics) + ("r-rsamtools" ,r-rsamtools) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/jotsetung/ensembldb") + (synopsis "Utilities to create and use Ensembl-based annotation databases") + (description + "The package provides functions to create and use transcript-centric +annotation databases/packages. The annotation for the databases are directly +fetched from Ensembl using their Perl API. The functionality and data is +similar to that of the TxDb packages from the @code{GenomicFeatures} package, +but, in addition to retrieve all gene/transcript models and annotations from +the database, the @code{ensembldb} package also provides a filter framework +allowing to retrieve annotations for specific entries like genes encoded on a +chromosome region or transcript models of lincRNA genes.") + ;; No version specified + (license license:lgpl3+))) + (define-public r-fastseg (package (name "r-fastseg") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b17ca0fabd..4be61522b6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9108,51 +9108,6 @@ (define-public r-mzr previously been used in XCMS.") (license license:artistic2.0))) -(define-public r-ensembldb - (package - (name "r-ensembldb") - (version "2.14.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ensembldb" version)) - (sha256 - (base32 - "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-curl" ,r-curl) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-protgenerics" ,r-protgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/jotsetung/ensembldb") - (synopsis "Utilities to create and use Ensembl-based annotation databases") - (description - "The package provides functions to create and use transcript-centric -annotation databases/packages. The annotation for the databases are directly -fetched from Ensembl using their Perl API. The functionality and data is -similar to that of the TxDb packages from the @code{GenomicFeatures} package, -but, in addition to retrieve all gene/transcript models and annotations from -the database, the @code{ensembldb} package also provides a filter framework -allowing to retrieve annotations for specific entries like genes encoded on a -chromosome region or transcript models of lincRNA genes.") - ;; No version specified - (license license:lgpl3+))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit v1.2.3 From 720d2694a5e50fac5d86f67a5faae61881ad4b38 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:05 +0200 Subject: gnu: r-mzr: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-mzr): Move from here... * gnu/packages/bioconductor.scm (r-mzr): ...to here. --- gnu/packages/bioconductor.scm | 62 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 61 ---------------------------------------- 2 files changed, 62 insertions(+), 61 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index eb0bcb22c6..08d4545257 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -36,6 +36,7 @@ (define-module (gnu packages bioconductor) #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages boost) #:use-module (gnu packages cran) #:use-module (gnu packages compression) #:use-module (gnu packages gcc) @@ -3256,6 +3257,67 @@ (define-public r-mzid specific parser.") (license license:gpl2+))) +(define-public r-mzr + (package + (name "r-mzr") + (version "2.24.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mzR" version)) + (sha256 + (base32 + "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "src/boost") + #t)))) + (properties `((upstream-name . "mzR"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-boost + (lambda _ + (substitute* "src/Makevars" + (("\\./boost/libs.*") "") + ;; This is to avoid having a plain directory on the list of + ;; libraries to link. + (("\\(RHDF5_LIBS\\)" match) + (string-append match "/libhdf5.a")) + (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ") + (("\\ARCH_OBJS=" line) + (string-append line + "\nBOOST_LIBS=-lboost_system -lboost_regex \ +-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) + #t))))) + (inputs + `(;; Our default boost package won't work here, unfortunately, even with + ;; mzR version 2.24.1. + ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources + ("zlib" ,zlib))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-ncdf4" ,r-ncdf4) + ("r-protgenerics" ,r-protgenerics) + ("r-rcpp" ,r-rcpp) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/sneumann/mzR/") + (synopsis "Parser for mass spectrometry data files") + (description + "The mzR package provides a unified API to the common file formats and +parsers available for mass spectrometry data. It comes with a wrapper for the +ISB random access parser for mass spectrometry mzXML, mzData and mzML files. +The package contains the original code written by the ISB, and a subset of the +proteowizard library for mzML and mzIdentML. The netCDF reading code has +previously been used in XCMS.") + (license license:artistic2.0))) + (define-public r-organismdbi (package (name "r-organismdbi") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4be61522b6..b356a76681 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9047,67 +9047,6 @@ (define-public r-protgenerics proteomics packages.") (license license:artistic2.0))) -(define-public r-mzr - (package - (name "r-mzr") - (version "2.24.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "mzR" version)) - (sha256 - (base32 - "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg")) - (modules '((guix build utils))) - (snippet - '(begin - (delete-file-recursively "src/boost") - #t)))) - (properties `((upstream-name . "mzR"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-system-boost - (lambda _ - (substitute* "src/Makevars" - (("\\./boost/libs.*") "") - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\(RHDF5_LIBS\\)" match) - (string-append match "/libhdf5.a")) - (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ") - (("\\ARCH_OBJS=" line) - (string-append line - "\nBOOST_LIBS=-lboost_system -lboost_regex \ --lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) - #t))))) - (inputs - `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.24.1. - ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources - ("zlib" ,zlib))) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-ncdf4" ,r-ncdf4) - ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/sneumann/mzR/") - (synopsis "Parser for mass spectrometry data files") - (description - "The mzR package provides a unified API to the common file formats and -parsers available for mass spectrometry data. It comes with a wrapper for the -ISB random access parser for mass spectrometry mzXML, mzData and mzML files. -The package contains the original code written by the ISB, and a subset of the -proteowizard library for mzML and mzIdentML. The netCDF reading code has -previously been used in XCMS.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit v1.2.3 From 900ef8fb1ea8a85966a1a81ea01a9f3670fc8c58 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:06 +0200 Subject: gnu: r-protgenerics: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-protgenerics): Move from here... * gnu/packages/bioconductor.scm (r-protgenerics): ...to here. --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ gnu/packages/bioinformatics.scm | 20 -------------------- 2 files changed, 20 insertions(+), 20 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 08d4545257..8e0182691b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3380,6 +3380,26 @@ (define-public r-pcamethods structure (pcaRes) to provide a common interface to the PCA results.") (license license:gpl3+))) +(define-public r-protgenerics + (package + (name "r-protgenerics") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ProtGenerics" version)) + (sha256 + (base32 + "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz")))) + (properties `((upstream-name . "ProtGenerics"))) + (build-system r-build-system) + (home-page "https://github.com/lgatto/ProtGenerics") + (synopsis "S4 generic functions for proteomics infrastructure") + (description + "This package provides S4 generic functions needed by Bioconductor +proteomics packages.") + (license license:artistic2.0))) + (define-public r-rbgl (package (name "r-rbgl") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b356a76681..ca0952895c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9027,26 +9027,6 @@ (define-public r-raremetals2 trait.") (license license:gpl3))) -(define-public r-protgenerics - (package - (name "r-protgenerics") - (version "1.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ProtGenerics" version)) - (sha256 - (base32 - "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz")))) - (properties `((upstream-name . "ProtGenerics"))) - (build-system r-build-system) - (home-page "https://github.com/lgatto/ProtGenerics") - (synopsis "S4 generic functions for proteomics infrastructure") - (description - "This package provides S4 generic functions needed by Bioconductor -proteomics packages.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit v1.2.3 From 621aa3b442341c81305d2d56835203ff517a7bb9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:07 +0200 Subject: gnu: r-sva: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-sva): Move from here... * gnu/packages/bioconductor.scm (r-sva): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8e0182691b..a4d99dd929 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3790,6 +3790,37 @@ (define-public r-summarizedexperiment samples.") (license license:artistic2.0))) +(define-public r-sva + (package + (name "r-sva") + (version "3.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "sva" version)) + (sha256 + (base32 + "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy")))) + (build-system r-build-system) + (propagated-inputs + `(("r-edger" ,r-edger) + ("r-genefilter" ,r-genefilter) + ("r-mgcv" ,r-mgcv) + ("r-biocparallel" ,r-biocparallel) + ("r-matrixstats" ,r-matrixstats) + ("r-limma" ,r-limma))) + (home-page "https://bioconductor.org/packages/sva") + (synopsis "Surrogate variable analysis") + (description + "This package contains functions for removing batch effects and other +unwanted variation in high-throughput experiment. It also contains functions +for identifying and building surrogate variables for high-dimensional data +sets. Surrogate variables are covariates constructed directly from +high-dimensional data like gene expression/RNA sequencing/methylation/brain +imaging data that can be used in subsequent analyses to adjust for unknown, +unmodeled, or latent sources of noise.") + (license license:artistic2.0))) + (define-public r-systempiper (package (name "r-systempiper") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ca0952895c..cb0fe505cb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8964,37 +8964,6 @@ (define-public r-methylkit TAB-Seq.") (license license:artistic2.0))) -(define-public r-sva - (package - (name "r-sva") - (version "3.38.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "sva" version)) - (sha256 - (base32 - "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy")))) - (build-system r-build-system) - (propagated-inputs - `(("r-edger" ,r-edger) - ("r-genefilter" ,r-genefilter) - ("r-mgcv" ,r-mgcv) - ("r-biocparallel" ,r-biocparallel) - ("r-matrixstats" ,r-matrixstats) - ("r-limma" ,r-limma))) - (home-page "https://bioconductor.org/packages/sva") - (synopsis "Surrogate variable analysis") - (description - "This package contains functions for removing batch effects and other -unwanted variation in high-throughput experiment. It also contains functions -for identifying and building surrogate variables for high-dimensional data -sets. Surrogate variables are covariates constructed directly from -high-dimensional data like gene expression/RNA sequencing/methylation/brain -imaging data that can be used in subsequent analyses to adjust for unknown, -unmodeled, or latent sources of noise.") - (license license:artistic2.0))) - (define-public r-raremetals2 (package (name "r-raremetals2") -- cgit v1.2.3 From c2a18aee16a59330a005bf6818df733a2f56c425 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:08 +0200 Subject: gnu: r-motifrg: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-motifrg): Move from here... * gnu/packages/bioconductor.scm (r-motifrg): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a4d99dd929..c9f72c5492 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3129,6 +3129,33 @@ (define-public r-limma different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-motifrg + (package + (name "r-motifrg") + (version "1.31.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "motifRG" version)) + (sha256 + (base32 + "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn")))) + (properties `((upstream-name . "motifRG"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-iranges" ,r-iranges) + ("r-seqlogo" ,r-seqlogo) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/motifRG") + (synopsis "Discover motifs in high throughput sequencing data") + (description + "This package provides tools for discriminative motif discovery in high +throughput genetic sequencing data sets using regression methods.") + (license license:artistic2.0))) + (define-public r-msnbase (package (name "r-msnbase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cb0fe505cb..8f011f0c78 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8046,33 +8046,6 @@ (define-public r-seqlogo Stephens (1990).") (license license:lgpl2.0+))) -(define-public r-motifrg - (package - (name "r-motifrg") - (version "1.31.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "motifRG" version)) - (sha256 - (base32 - "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn")))) - (properties `((upstream-name . "motifRG"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-iranges" ,r-iranges) - ("r-seqlogo" ,r-seqlogo) - ("r-xvector" ,r-xvector))) - (home-page "https://bioconductor.org/packages/motifRG") - (synopsis "Discover motifs in high throughput sequencing data") - (description - "This package provides tools for discriminative motif discovery in high -throughput genetic sequencing data sets using regression methods.") - (license license:artistic2.0))) - (define-public r-zlibbioc (package (name "r-zlibbioc") -- cgit v1.2.3 From 0006a664155c7d556ac773b254fd09205412c172 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:09 +0200 Subject: gnu: r-seqlogo: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-seqlogo): Move from here... * gnu/packages/bioconductor.scm (r-seqlogo): ...to here. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 23 ----------------------- 2 files changed, 23 insertions(+), 23 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c9f72c5492..b53267e80d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3652,6 +3652,29 @@ (define-public r-samr ;; Any version of the LGPL (license license:lgpl3+))) +(define-public r-seqlogo + (package + (name "r-seqlogo") + (version "1.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "seqLogo" version)) + (sha256 + (base32 + "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1")))) + (properties `((upstream-name . "seqLogo"))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/seqLogo") + (synopsis "Sequence logos for DNA sequence alignments") + (description + "seqLogo takes the position weight matrix of a DNA sequence motif and +plots the corresponding sequence logo as introduced by Schneider and +Stephens (1990).") + (license license:lgpl2.0+))) + (define-public r-seqpattern (package (name "r-seqpattern") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8f011f0c78..832de0baad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8023,29 +8023,6 @@ (define-public r-phantompeakqualtools characteristic tag shift values in these assays.") (license license:bsd-3))) -(define-public r-seqlogo - (package - (name "r-seqlogo") - (version "1.56.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "seqLogo" version)) - (sha256 - (base32 - "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1")))) - (properties `((upstream-name . "seqLogo"))) - (build-system r-build-system) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/seqLogo") - (synopsis "Sequence logos for DNA sequence alignments") - (description - "seqLogo takes the position weight matrix of a DNA sequence motif and -plots the corresponding sequence logo as introduced by Schneider and -Stephens (1990).") - (license license:lgpl2.0+))) - (define-public r-zlibbioc (package (name "r-zlibbioc") -- cgit v1.2.3 From e0c81584ea47ebce218a9ef37accab0889860fc1 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:10 +0200 Subject: gnu: r-zlibbioc: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-zlibbioc): Move from here... * gnu/packages/bioconductor.scm (r-zlibbioc): ...to here. --- gnu/packages/bioconductor.scm | 19 +++++++++++++++++++ gnu/packages/bioinformatics.scm | 19 ------------------- 2 files changed, 19 insertions(+), 19 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b53267e80d..ea4e373b49 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4068,6 +4068,25 @@ (define-public r-xvector \"externally\" (behind an R external pointer, or on disk).") (license license:artistic2.0))) +(define-public r-zlibbioc + (package + (name "r-zlibbioc") + (version "1.36.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "zlibbioc" version)) + (sha256 + (base32 + "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg")))) + (properties + `((upstream-name . "zlibbioc"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/zlibbioc") + (synopsis "Provider for zlib-1.2.5 to R packages") + (description "This package uses the source code of zlib-1.2.5 to create +libraries for systems that do not have these available via other means.") + (license license:artistic2.0))) + (define-public r-geneplotter (package (name "r-geneplotter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 832de0baad..3bd982ae31 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8023,25 +8023,6 @@ (define-public r-phantompeakqualtools characteristic tag shift values in these assays.") (license license:bsd-3))) -(define-public r-zlibbioc - (package - (name "r-zlibbioc") - (version "1.36.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "zlibbioc" version)) - (sha256 - (base32 - "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg")))) - (properties - `((upstream-name . "zlibbioc"))) - (build-system r-build-system) - (home-page "https://bioconductor.org/packages/zlibbioc") - (synopsis "Provider for zlib-1.2.5 to R packages") - (description "This package uses the source code of zlib-1.2.5 to create -libraries for systems that do not have these available via other means.") - (license license:artistic2.0))) - (define-public r-r4rna (package (name "r-r4rna") -- cgit v1.2.3 From 043c309d154a69455e0fa7624afa98b912bffb6d Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:11 +0200 Subject: gnu: r-rhtslib: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-rhtslib): Move from here... * gnu/packages/bioconductor.scm (r-rhtslib): ...to here. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 32 insertions(+), 31 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ea4e373b49..cb42c0bed2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -39,6 +39,7 @@ (define-module (gnu packages bioconductor) #:use-module (gnu packages boost) #:use-module (gnu packages cran) #:use-module (gnu packages compression) + #:use-module (gnu packages curl) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) #:use-module (gnu packages graphviz) @@ -3037,6 +3038,37 @@ (define-public r-hpar the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-rhtslib + (package + (name "r-rhtslib") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Rhtslib" version)) + (sha256 + (base32 + "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4")))) + (properties `((upstream-name . "Rhtslib"))) + (build-system r-build-system) + ;; Without this a temporary directory ends up in the Rhtslib.so binary, + ;; which makes R abort the build. + (arguments '(#:configure-flags '("--no-staged-install"))) + (propagated-inputs + `(("curl" ,curl) + ("zlib" ,zlib) ; packages using rhtslib need to link with zlib + ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("r-knitr" ,r-knitr))) + (home-page "https://github.com/nhayden/Rhtslib") + (synopsis "High-throughput sequencing library as an R package") + (description + "This package provides the HTSlib C library for high-throughput +nucleotide sequence analysis. The package is primarily useful to developers +of other R packages who wish to make use of HTSlib.") + (license license:lgpl2.0+))) + (define-public r-impute (package (name "r-impute") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3bd982ae31..fd83c4dd48 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8046,37 +8046,6 @@ (define-public r-r4rna secondary structure and comparative analysis in R.") (license license:gpl3+))) -(define-public r-rhtslib - (package - (name "r-rhtslib") - (version "1.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "Rhtslib" version)) - (sha256 - (base32 - "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4")))) - (properties `((upstream-name . "Rhtslib"))) - (build-system r-build-system) - ;; Without this a temporary directory ends up in the Rhtslib.so binary, - ;; which makes R abort the build. - (arguments '(#:configure-flags '("--no-staged-install"))) - (propagated-inputs - `(("curl" ,curl) - ("zlib" ,zlib) ; packages using rhtslib need to link with zlib - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) - (home-page "https://github.com/nhayden/Rhtslib") - (synopsis "High-throughput sequencing library as an R package") - (description - "This package provides the HTSlib C library for high-throughput -nucleotide sequence analysis. The package is primarily useful to developers -of other R packages who wish to make use of HTSlib.") - (license license:lgpl2.0+))) - (define-public r-bamsignals (package (name "r-bamsignals") -- cgit v1.2.3 From 45b6db4fb4b6963be6fca4dc747d763673edce3c Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:12 +0200 Subject: gnu: r-bamsignals: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-bamsignals): Move from here... * gnu/packages/bioconductor.scm (r-bamsignals): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index cb42c0bed2..382e3b6d28 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2109,6 +2109,36 @@ (define-public r-aroma-light classes.") (license license:gpl2+))) +(define-public r-bamsignals + (package + (name "r-bamsignals") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bamsignals" version)) + (sha256 + (base32 + "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcpp" ,r-rcpp) + ("r-rhtslib" ,r-rhtslib) + ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/bamsignals") + (synopsis "Extract read count signals from bam files") + (description + "This package efficiently obtains count vectors from indexed bam +files. It counts the number of nucleotide sequence reads in given genomic +ranges and it computes reads profiles and coverage profiles. It also handles +paired-end data.") + (license license:gpl2+))) + (define-public r-biobase (package (name "r-biobase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fd83c4dd48..998541434f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8046,36 +8046,6 @@ (define-public r-r4rna secondary structure and comparative analysis in R.") (license license:gpl3+))) -(define-public r-bamsignals - (package - (name "r-bamsignals") - (version "1.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "bamsignals" version)) - (sha256 - (base32 - "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/bamsignals") - (synopsis "Extract read count signals from bam files") - (description - "This package efficiently obtains count vectors from indexed bam -files. It counts the number of nucleotide sequence reads in given genomic -ranges and it computes reads profiles and coverage profiles. It also handles -paired-end data.") - (license license:gpl2+))) - (define-public r-rcas (package (name "r-rcas") -- cgit v1.2.3 From 7360dea62449d5c4f5ce897ee8f642090326ebc9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:13 +0200 Subject: gnu: r-rcas: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-rcas): Move from here... * gnu/packages/bioconductor.scm (r-rcas): ...to here. --- gnu/packages/bioconductor.scm | 49 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 49 ----------------------------------------- 2 files changed, 49 insertions(+), 49 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 382e3b6d28..ca9e15d53e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3512,6 +3512,55 @@ (define-public r-rbgl the graph algorithms contained in the Boost library.") (license license:artistic2.0))) +(define-public r-rcas + (package + (name "r-rcas") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "RCAS" version)) + (sha256 + (base32 + "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m")))) + (properties `((upstream-name . "RCAS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-cowplot" ,r-cowplot) + ("r-data-table" ,r-data-table) + ("r-dt" ,r-dt) + ("r-genomation" ,r-genomation) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-ggseqlogo" ,r-ggseqlogo) + ("r-gprofiler2" ,r-gprofiler2) + ("r-iranges" ,r-iranges) + ("r-pbapply" ,r-pbapply) + ("r-pheatmap" ,r-pheatmap) + ("r-plotly" ,r-plotly) + ("r-plotrix" ,r-plotrix) + ("r-proxy" ,r-proxy) + ("r-ranger" ,r-ranger) + ("r-rsqlite" ,r-rsqlite) + ("r-rtracklayer" ,r-rtracklayer) + ("r-rmarkdown" ,r-rmarkdown) + ("r-s4vectors" ,r-s4vectors) + ("pandoc" ,pandoc))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (synopsis "RNA-centric annotation system") + (description + "RCAS aims to be a standalone RNA-centric annotation system that provides +intuitive reports and publication-ready graphics. This package provides the R +library implementing most of the pipeline's features.") + (home-page "https://github.com/BIMSBbioinfo/RCAS") + (license license:artistic2.0))) + (define-public r-regioner (package (name "r-regioner") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 998541434f..e9eebd35b5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8046,55 +8046,6 @@ (define-public r-r4rna secondary structure and comparative analysis in R.") (license license:gpl3+))) -(define-public r-rcas - (package - (name "r-rcas") - (version "1.16.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "RCAS" version)) - (sha256 - (base32 - "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m")))) - (properties `((upstream-name . "RCAS"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-cowplot" ,r-cowplot) - ("r-data-table" ,r-data-table) - ("r-dt" ,r-dt) - ("r-genomation" ,r-genomation) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggseqlogo" ,r-ggseqlogo) - ("r-gprofiler2" ,r-gprofiler2) - ("r-iranges" ,r-iranges) - ("r-pbapply" ,r-pbapply) - ("r-pheatmap" ,r-pheatmap) - ("r-plotly" ,r-plotly) - ("r-plotrix" ,r-plotrix) - ("r-proxy" ,r-proxy) - ("r-ranger" ,r-ranger) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rmarkdown" ,r-rmarkdown) - ("r-s4vectors" ,r-s4vectors) - ("pandoc" ,pandoc))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (synopsis "RNA-centric annotation system") - (description - "RCAS aims to be a standalone RNA-centric annotation system that provides -intuitive reports and publication-ready graphics. This package provides the R -library implementing most of the pipeline's features.") - (home-page "https://github.com/BIMSBbioinfo/RCAS") - (license license:artistic2.0))) - (define-public rcas-web (package (name "rcas-web") -- cgit v1.2.3 From bf8f50295696a95a0ae3dca14188709b4330efac Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:14 +0200 Subject: gnu: r-mutationalpatterns: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-mutationalpatterns): Move from here... * gnu/packages/bioconductor.scm (r-mutationalpatterns): ...to here. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 45 ----------------------------------------- 2 files changed, 45 insertions(+), 45 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ca9e15d53e..f66ba6ce5f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3218,6 +3218,51 @@ (define-public r-motifrg throughput genetic sequencing data sets using regression methods.") (license license:artistic2.0))) +(define-public r-mutationalpatterns + (package + (name "r-mutationalpatterns") + (version "3.0.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MutationalPatterns" version)) + (sha256 + (base32 + "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ;; These two packages are suggested packages + ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-cowplot" ,r-cowplot) + ("r-dplyr" ,r-dplyr) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggalluvial" ,r-ggalluvial) + ("r-ggdendro" ,r-ggdendro) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-magrittr" ,r-magrittr) + ("r-nmf" ,r-nmf) + ("r-pracma" ,r-pracma) + ("r-purrr" ,r-purrr) + ("r-s4vectors" ,r-s4vectors) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/MutationalPatterns/") + (synopsis "Extract and visualize mutational patterns in genomic data") + (description "This package provides an extensive toolset for the +characterization and visualization of a wide range of mutational patterns +in SNV base substitution data.") + (license license:expat))) + (define-public r-msnbase (package (name "r-msnbase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e9eebd35b5..2fc46c7978 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8097,51 +8097,6 @@ (define-public rcas-web @dfn{RNA-centric annotation system} (RCAS).") (license license:agpl3+))) -(define-public r-mutationalpatterns - (package - (name "r-mutationalpatterns") - (version "3.0.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "MutationalPatterns" version)) - (sha256 - (base32 - "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35")))) - (build-system r-build-system) - (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ;; These two packages are suggested packages - ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggalluvial" ,r-ggalluvial) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-magrittr" ,r-magrittr) - ("r-nmf" ,r-nmf) - ("r-pracma" ,r-pracma) - ("r-purrr" ,r-purrr) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-variantannotation" ,r-variantannotation))) - (home-page "https://bioconductor.org/packages/MutationalPatterns/") - (synopsis "Extract and visualize mutational patterns in genomic data") - (description "This package provides an extensive toolset for the -characterization and visualization of a wide range of mutational patterns -in SNV base substitution data.") - (license license:expat))) - (define-public r-chipkernels (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372") (revision "1")) -- cgit v1.2.3 From b6e84d30ebd5b5bd1bb1027a6199601b96580fa9 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:15 +0200 Subject: gnu: r-tximport: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-tximport): Move from here... * gnu/packages/bioconductor.scm (r-tximport): ...to here. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 24 ------------------------ 2 files changed, 24 insertions(+), 24 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f66ba6ce5f..f276749abf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4114,6 +4114,30 @@ (define-public r-topgo ;; Any version of the LGPL applies. (license license:lgpl2.1+))) +(define-public r-tximport + (package + (name "r-tximport") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tximport" version)) + (sha256 + (base32 + "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/tximport") + (synopsis "Import and summarize transcript-level estimates for gene-level analysis") + (description + "This package provides tools to import transcript-level abundance, +estimated counts and transcript lengths, and to summarize them into matrices +for use with downstream gene-level analysis packages. Average transcript +length, weighted by sample-specific transcript abundance estimates, is +provided as a matrix which can be used as an offset for different expression +of gene-level counts.") + (license license:gpl2+))) + (define-public r-variantannotation (package (name "r-variantannotation") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2fc46c7978..fcaed708a6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8164,30 +8164,6 @@ (define-public r-seqgl factors bound at the specific regions.") (license license:gpl2+))) -(define-public r-tximport - (package - (name "r-tximport") - (version "1.18.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "tximport" version)) - (sha256 - (base32 - "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34")))) - (build-system r-build-system) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/tximport") - (synopsis "Import and summarize transcript-level estimates for gene-level analysis") - (description - "This package provides tools to import transcript-level abundance, -estimated counts and transcript lengths, and to summarize them into matrices -for use with downstream gene-level analysis packages. Average transcript -length, weighted by sample-specific transcript abundance estimates, is -provided as a matrix which can be used as an offset for different expression -of gene-level counts.") - (license license:gpl2+))) - (define-public r-rhdf5filters (package (name "r-rhdf5filters") -- cgit v1.2.3 From 67e99369c1f96b3eda703702de0fdcfa17d34872 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:16 +0200 Subject: gnu: r-rhdf5filters: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-rhdf5filters): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5filters): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f276749abf..faa464d5b7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3687,6 +3687,32 @@ (define-public r-reportingtools browser.") (license license:artistic2.0))) +(define-public r-rhdf5filters + (package + (name "r-rhdf5filters") + (version "1.2.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "rhdf5filters" version)) + (sha256 + (base32 + "1bjlgc76vx0z81s8vci9ln1d2s3b157qnm32xs36mnyjk31ivasz")))) + (properties `((upstream-name . "rhdf5filters"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rhdf5lib" ,r-rhdf5lib))) + (inputs + `(("zlib" ,zlib))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/grimbough/rhdf5filters") + (synopsis "HDF5 compression filters") + (description + "This package provides a collection of compression filters for use with +HDF5 datasets.") + (license license:bsd-2))) + (define-public r-rsamtools (package (name "r-rsamtools") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fcaed708a6..24973d3cb4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8164,32 +8164,6 @@ (define-public r-seqgl factors bound at the specific regions.") (license license:gpl2+))) -(define-public r-rhdf5filters - (package - (name "r-rhdf5filters") - (version "1.2.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "rhdf5filters" version)) - (sha256 - (base32 - "1bjlgc76vx0z81s8vci9ln1d2s3b157qnm32xs36mnyjk31ivasz")))) - (properties `((upstream-name . "rhdf5filters"))) - (build-system r-build-system) - (propagated-inputs - `(("r-rhdf5lib" ,r-rhdf5lib))) - (inputs - `(("zlib" ,zlib))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/grimbough/rhdf5filters") - (synopsis "HDF5 compression filters") - (description - "This package provides a collection of compression filters for use with -HDF5 datasets.") - (license license:bsd-2))) - (define-public r-rhdf5 (package (name "r-rhdf5") -- cgit v1.2.3 From cc1dbea883fed7515130144a2413c49c11c5352f Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:17 +0200 Subject: gnu: r-annotationfilter: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-annotationfilter): Move from here... * gnu/packages/bioconductor.scm (r-annotationfilter): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index faa464d5b7..a6d0350da9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2009,6 +2009,32 @@ (define-public r-annotationdbi annotation data packages using SQLite data storage.") (license license:artistic2.0))) +(define-public r-annotationfilter + (package + (name "r-annotationfilter") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationFilter" version)) + (sha256 + (base32 + "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9")))) + (properties + `((upstream-name . "AnnotationFilter"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicranges" ,r-genomicranges) + ("r-lazyeval" ,r-lazyeval))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/Bioconductor/AnnotationFilter") + (synopsis "Facilities for filtering Bioconductor annotation resources") + (description + "This package provides classes and other infrastructure to implement +filters for manipulating Bioconductor annotation resources. The filters are +used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") + (license license:artistic2.0))) + (define-public r-annotationforge (package (name "r-annotationforge") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 24973d3cb4..c144344dc7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8203,32 +8203,6 @@ (define-public r-rhdf5 the available RAM.") (license license:artistic2.0))) -(define-public r-annotationfilter - (package - (name "r-annotationfilter") - (version "1.14.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "AnnotationFilter" version)) - (sha256 - (base32 - "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9")))) - (properties - `((upstream-name . "AnnotationFilter"))) - (build-system r-build-system) - (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-lazyeval" ,r-lazyeval))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/Bioconductor/AnnotationFilter") - (synopsis "Facilities for filtering Bioconductor annotation resources") - (description - "This package provides classes and other infrastructure to implement -filters for manipulating Bioconductor annotation resources. The filters are -used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") - (license license:artistic2.0))) - (define-public emboss (package (name "emboss") -- cgit v1.2.3 From 0eaa75c8117b4e91475d7c4ad9960b925cef5d56 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:18 +0200 Subject: gnu: r-rhdf5: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-rhdf5): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5): ...to here. --- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 39 --------------------------------------- 2 files changed, 39 insertions(+), 39 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a6d0350da9..5ae045456a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3713,6 +3713,45 @@ (define-public r-reportingtools browser.") (license license:artistic2.0))) +(define-public r-rhdf5 + (package + (name "r-rhdf5") + (version "2.34.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "rhdf5" version)) + (sha256 + (base32 + "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-linking + (lambda _ + (substitute* "src/Makevars" + ;; This is to avoid having a plain directory on the list of + ;; libraries to link. + (("\\(RHDF5_LIBS\\)" match) + (string-append match "/libhdf5.a"))) + #t))))) + (propagated-inputs + `(("r-rhdf5filters" ,r-rhdf5filters) + ("r-rhdf5lib" ,r-rhdf5lib))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/rhdf5") + (synopsis "HDF5 interface to R") + (description + "This R/Bioconductor package provides an interface between HDF5 and R. +HDF5's main features are the ability to store and access very large and/or +complex datasets and a wide variety of metadata on mass storage (disk) through +a completely portable file format. The rhdf5 package is thus suited for the +exchange of large and/or complex datasets between R and other software +package, and for letting R applications work on datasets that are larger than +the available RAM.") + (license license:artistic2.0))) + (define-public r-rhdf5filters (package (name "r-rhdf5filters") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c144344dc7..a241a83c80 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8164,45 +8164,6 @@ (define-public r-seqgl factors bound at the specific regions.") (license license:gpl2+))) -(define-public r-rhdf5 - (package - (name "r-rhdf5") - (version "2.34.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "rhdf5" version)) - (sha256 - (base32 - "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi")))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-linking - (lambda _ - (substitute* "src/Makevars" - ;; This is to avoid having a plain directory on the list of - ;; libraries to link. - (("\\(RHDF5_LIBS\\)" match) - (string-append match "/libhdf5.a"))) - #t))))) - (propagated-inputs - `(("r-rhdf5filters" ,r-rhdf5filters) - ("r-rhdf5lib" ,r-rhdf5lib))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/rhdf5") - (synopsis "HDF5 interface to R") - (description - "This R/Bioconductor package provides an interface between HDF5 and R. -HDF5's main features are the ability to store and access very large and/or -complex datasets and a wide variety of metadata on mass storage (disk) through -a completely portable file format. The rhdf5 package is thus suited for the -exchange of large and/or complex datasets between R and other software -package, and for letting R applications work on datasets that are larger than -the available RAM.") - (license license:artistic2.0))) - (define-public emboss (package (name "emboss") -- cgit v1.2.3 From 31e50e1f48308a78a04f9aced53f2c2706660b31 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:19 +0200 Subject: gnu: r-chipseq: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-chipseq): Move from here... * gnu/packages/bioconductor.scm (r-chipseq): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5ae045456a..2a7872cbd2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2411,6 +2411,32 @@ (define-public r-category analysis.") (license license:artistic2.0))) +(define-public r-chipseq + (package + (name "r-chipseq") + (version "1.40.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "chipseq" version)) + (sha256 + (base32 + "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-s4vectors" ,r-s4vectors) + ("r-shortread" ,r-shortread))) + (home-page "https://bioconductor.org/packages/chipseq") + (synopsis "Package for analyzing ChIPseq data") + (description + "This package provides tools for processing short read data from ChIPseq +experiments.") + (license license:artistic2.0))) + (define-public r-complexheatmap (package (name "r-complexheatmap") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a241a83c80..aa92ae3916 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8486,32 +8486,6 @@ (define-public variant-tools manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-chipseq - (package - (name "r-chipseq") - (version "1.40.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "chipseq" version)) - (sha256 - (base32 - "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-s4vectors" ,r-s4vectors) - ("r-shortread" ,r-shortread))) - (home-page "https://bioconductor.org/packages/chipseq") - (synopsis "Package for analyzing ChIPseq data") - (description - "This package provides tools for processing short read data from ChIPseq -experiments.") - (license license:artistic2.0))) - (define-public r-copyhelper (package (name "r-copyhelper") -- cgit v1.2.3 From 36cb01066cc03b2d341b55f21ebba2156518a560 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:20 +0200 Subject: gnu: r-copyhelper: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-copyhelper): Move from here... * gnu/packages/bioconductor.scm (r-copyhelper): ...to here. [source]: Repalce 'string-append' by 'bioconductor-uri' with 'experiment. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 24 insertions(+), 26 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2a7872cbd2..9118642e66 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1128,6 +1128,30 @@ (define-public r-chipseeker annotation, distance to TSS, and overlap of peaks or genes.") (license license:artistic2.0))) +(define-public r-copyhelper + (package + (name "r-copyhelper") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CopyhelpeR" version 'experiment)) + (sha256 + (base32 + "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq")))) + (properties `((upstream-name . "CopyhelpeR"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/CopyhelpeR/") + (synopsis "Helper files for CopywriteR") + (description + "This package contains the helper files that are required to run the +Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content +and mappability files for the reference genomes hg18, hg19, hg38, mm9 and +mm10. In addition, it contains a blacklist filter to remove regions that +display copy number variation. Files are stored as GRanges objects from the +GenomicRanges Bioconductor package.") + (license license:gpl2))) + (define-public r-genelendatabase (package (name "r-genelendatabase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index aa92ae3916..85e586a174 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8486,32 +8486,6 @@ (define-public variant-tools manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-copyhelper - (package - (name "r-copyhelper") - (version "1.6.0") - (source - (origin - (method url-fetch) - (uri (string-append "https://bioconductor.org/packages/release/" - "data/experiment/src/contrib/CopyhelpeR_" - version ".tar.gz")) - (sha256 - (base32 - "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq")))) - (properties `((upstream-name . "CopyhelpeR"))) - (build-system r-build-system) - (home-page "https://bioconductor.org/packages/CopyhelpeR/") - (synopsis "Helper files for CopywriteR") - (description - "This package contains the helper files that are required to run the -Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content -and mappability files for the reference genomes hg18, hg19, hg38, mm9 and -mm10. In addition, it contains a blacklist filter to remove regions that -display copy number variation. Files are stored as GRanges objects from the -GenomicRanges Bioconductor package.") - (license license:gpl2))) - (define-public r-copywriter (package (name "r-copywriter") -- cgit v1.2.3 From 7ab44aeed61b1e0a3a048bf2b991180d76a97aff Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:21 +0200 Subject: gnu: r-copywriter: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-copywriter): Move from here... * gnu/packages/bioconductor.scm (r-copywriter): ...to here. --- gnu/packages/bioconductor.scm | 40 ++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 40 ---------------------------------------- 2 files changed, 40 insertions(+), 40 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9118642e66..fae6073446 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2500,6 +2500,46 @@ (define-public r-complexheatmap self-defined annotation graphics.") (license license:gpl2+))) +(define-public r-copywriter + (package + (name "r-copywriter") + (version "2.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CopywriteR" version)) + (sha256 + (base32 + "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f")))) + (properties `((upstream-name . "CopywriteR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-chipseq" ,r-chipseq) + ("r-copyhelper" ,r-copyhelper) + ("r-data-table" ,r-data-table) + ("r-dnacopy" ,r-dnacopy) + ("r-futile-logger" ,r-futile-logger) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-iranges" ,r-iranges) + ("r-matrixstats" ,r-matrixstats) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/PeeperLab/CopywriteR") + (synopsis "Copy number information from targeted sequencing") + (description + "CopywriteR extracts DNA copy number information from targeted sequencing +by utilizing off-target reads. It allows for extracting uniformly distributed +copy number information, can be used without reference, and can be applied to +sequencing data obtained from various techniques including chromatin +immunoprecipitation and target enrichment on small gene panels. Thereby, +CopywriteR constitutes a widely applicable alternative to available copy +number detection tools.") + (license license:gpl2))) + (define-public r-deseq (package (name "r-deseq") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 85e586a174..abfaa3d4af 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8486,46 +8486,6 @@ (define-public variant-tools manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-copywriter - (package - (name "r-copywriter") - (version "2.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "CopywriteR" version)) - (sha256 - (base32 - "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f")))) - (properties `((upstream-name . "CopywriteR"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-chipseq" ,r-chipseq) - ("r-copyhelper" ,r-copyhelper) - ("r-data-table" ,r-data-table) - ("r-dnacopy" ,r-dnacopy) - ("r-futile-logger" ,r-futile-logger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://github.com/PeeperLab/CopywriteR") - (synopsis "Copy number information from targeted sequencing") - (description - "CopywriteR extracts DNA copy number information from targeted sequencing -by utilizing off-target reads. It allows for extracting uniformly distributed -copy number information, can be used without reference, and can be applied to -sequencing data obtained from various techniques including chromatin -immunoprecipitation and target enrichment on small gene panels. Thereby, -CopywriteR constitutes a widely applicable alternative to available copy -number detection tools.") - (license license:gpl2))) - (define-public r-methylkit (package (name "r-methylkit") -- cgit v1.2.3 From c294c0d782bf36a88e24eb4efcd2fbbf8209ace2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 21 May 2021 22:26:22 +0200 Subject: gnu: r-methylkit: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-methylkit): Move from here... * gnu/packages/bioconductor.scm (r-methylkit): ...to here. --- gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 47 ----------------------------------------- 2 files changed, 47 insertions(+), 47 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fae6073446..196ee22e25 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3307,6 +3307,53 @@ (define-public r-limma different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-methylkit + (package + (name "r-methylkit") + (version "1.16.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "methylKit" version)) + (sha256 + (base32 + "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3")))) + (properties `((upstream-name . "methylKit"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-emdbook" ,r-emdbook) + ("r-fastseg" ,r-fastseg) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-iranges" ,r-iranges) + ("r-kernsmooth" ,r-kernsmooth) + ("r-limma" ,r-limma) + ("r-mclust" ,r-mclust) + ("r-mgcv" ,r-mgcv) + ("r-qvalue" ,r-qvalue) + ("r-r-utils" ,r-r-utils) + ("r-rcpp" ,r-rcpp) + ("r-rhtslib" ,r-rhtslib) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://github.com/al2na/methylKit") + (synopsis + "DNA methylation analysis from high-throughput bisulfite sequencing results") + (description + "MethylKit is an R package for DNA methylation analysis and annotation +from high-throughput bisulfite sequencing. The package is designed to deal +with sequencing data from @dfn{Reduced representation bisulfite +sequencing} (RRBS) and its variants, but also target-capture methods and whole +genome bisulfite sequencing. It also has functions to analyze base-pair +resolution 5hmC data from experimental protocols such as oxBS-Seq and +TAB-Seq.") + (license license:artistic2.0))) + (define-public r-motifrg (package (name "r-motifrg") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index abfaa3d4af..11dbad5a22 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8486,53 +8486,6 @@ (define-public variant-tools manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-methylkit - (package - (name "r-methylkit") - (version "1.16.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "methylKit" version)) - (sha256 - (base32 - "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3")))) - (properties `((upstream-name . "methylKit"))) - (build-system r-build-system) - (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-emdbook" ,r-emdbook) - ("r-fastseg" ,r-fastseg) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-limma" ,r-limma) - ("r-mclust" ,r-mclust) - ("r-mgcv" ,r-mgcv) - ("r-qvalue" ,r-qvalue) - ("r-r-utils" ,r-r-utils) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes - (home-page "https://github.com/al2na/methylKit") - (synopsis - "DNA methylation analysis from high-throughput bisulfite sequencing results") - (description - "MethylKit is an R package for DNA methylation analysis and annotation -from high-throughput bisulfite sequencing. The package is designed to deal -with sequencing data from @dfn{Reduced representation bisulfite -sequencing} (RRBS) and its variants, but also target-capture methods and whole -genome bisulfite sequencing. It also has functions to analyze base-pair -resolution 5hmC data from experimental protocols such as oxBS-Seq and -TAB-Seq.") - (license license:artistic2.0))) - (define-public r-raremetals2 (package (name "r-raremetals2") -- cgit v1.2.3 From b0ecd6cea90838018744bfad15662abf8f1b0025 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 15:46:30 +0200 Subject: gnu: r-phantompeakqualtools: Let-bind commit, set revision to 1. * gnu/packages/bioinformatics.scm (r-phantompeakqualtools): Bind the commit outside of the package value. [version]: Use git-version. [source]: Use git-file-name. --- gnu/packages/bioinformatics.scm | 86 +++++++++++++++++++++-------------------- 1 file changed, 44 insertions(+), 42 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 11dbad5a22..a7ff938647 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7977,51 +7977,53 @@ (define-public r-spp (license license:gpl2))) (define-public r-phantompeakqualtools - (package - (name "r-phantompeakqualtools") - (version "1.2.2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/kundajelab/phantompeakqualtools") - (commit "8d2b2d18c686d894ef5908b37da7adf72a07ef42"))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "00anrvcwsp02d98qhj1xpj85644h2pp4kfzq6dgbmwmdr6jvy7p4")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; There are no tests. - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((script (string-append (assoc-ref outputs "out") - "/share/scripts"))) - (install-file "run_spp.R" script))))))) - (inputs - `(("r" ,r-minimal))) - (propagated-inputs - `(("r-catools" ,r-catools) - ("r-snow" ,r-snow) - ("r-snowfall" ,r-snowfall) - ("r-bitops" ,r-bitops) - ("r-rsamtools" ,r-rsamtools) - ("r-spp" ,r-spp) - ("gawk" ,gawk) - ("samtools" ,samtools) - ("boost" ,boost) - ("gzip" ,gzip))) - (home-page "https://github.com/kundajelab/phantompeakqualtools") - (synopsis "Informative enrichment for ChIP-seq data") - (description "This package computes informative enrichment and quality + (let ((commit "8d2b2d18c686d894ef5908b37da7adf72a07ef42") + (revision "1")) + (package + (name "r-phantompeakqualtools") + (version (git-version "1.2.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kundajelab/phantompeakqualtools") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00anrvcwsp02d98qhj1xpj85644h2pp4kfzq6dgbmwmdr6jvy7p4")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests. + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((script (string-append (assoc-ref outputs "out") + "/share/scripts"))) + (install-file "run_spp.R" script))))))) + (inputs + `(("r" ,r-minimal))) + (propagated-inputs + `(("r-catools" ,r-catools) + ("r-snow" ,r-snow) + ("r-snowfall" ,r-snowfall) + ("r-bitops" ,r-bitops) + ("r-rsamtools" ,r-rsamtools) + ("r-spp" ,r-spp) + ("gawk" ,gawk) + ("samtools" ,samtools) + ("boost" ,boost) + ("gzip" ,gzip))) + (home-page "https://github.com/kundajelab/phantompeakqualtools") + (synopsis "Informative enrichment for ChIP-seq data") + (description "This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.") - (license license:bsd-3))) + (license license:bsd-3)))) (define-public r-r4rna (package -- cgit v1.2.3 From a6e7afd4d55cc790aacbda64a327cb9f38a0d0f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 15:53:20 +0200 Subject: gnu: r-spp: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-spp): Move from here... * gnu/packages/bioconductor.scm (r-spp): ...to here. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 24 ------------------------ 2 files changed, 26 insertions(+), 24 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ba2bffe23e..5f594b85a7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13163,6 +13163,32 @@ (define-public r-abn statistical dependencies in messy, complex data.") (license license:gpl2+))) +;; This is a CRAN package, but it depends on r-rsamtools, which is a +;; Bioconductor package. +(define-public r-spp + (package + (name "r-spp") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (cran-uri "spp" version)) + (sha256 + (base32 + "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w")))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-catools" ,r-catools) + ("r-rcpp" ,r-rcpp) + ("r-rsamtools" ,r-rsamtools))) + (home-page "https://cran.r-project.org/web/packages/spp/") + (synopsis "ChIP-Seq processing pipeline") + (description "This package provides tools for analysis of ChIP-seq and +other functional sequencing data.") + (license license:gpl2))) + (define-public r-pathview (package (name "r-pathview") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a7ff938647..27e86b0a3b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7952,30 +7952,6 @@ (define-public bio-vcf (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-spp - (package - (name "r-spp") - (version "1.16.0") - (source (origin - (method url-fetch) - (uri (cran-uri "spp" version)) - (sha256 - (base32 - "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w")))) - (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-bh" ,r-bh) - ("r-catools" ,r-catools) - ("r-rcpp" ,r-rcpp) - ("r-rsamtools" ,r-rsamtools))) - (home-page "https://cran.r-project.org/web/packages/spp/") - (synopsis "ChIP-Seq processing pipeline") - (description "This package provides tools for analysis of ChIP-seq and -other functional sequencing data.") - (license license:gpl2))) - (define-public r-phantompeakqualtools (let ((commit "8d2b2d18c686d894ef5908b37da7adf72a07ef42") (revision "1")) -- cgit v1.2.3 From f383f9e3111c1708ee85b1acec60a1ff657c0aa6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 16:08:12 +0200 Subject: gnu: filevercmp: Use git-version. * gnu/packages/bioinformatics.scm (filevercmp)[version]: Use git-version; bind "revision" in outer let. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 27e86b0a3b..3ec0d0d301 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8347,10 +8347,11 @@ (define-public pepr (license license:gpl3+))) (define-public filevercmp - (let ((commit "1a9b779b93d0b244040274794d402106907b71b7")) + (let ((commit "1a9b779b93d0b244040274794d402106907b71b7") + (revision "1")) (package (name "filevercmp") - (version (string-append "0-1." (string-take commit 7))) + (version (git-version "0" revision commit)) (source (origin (method git-fetch) (uri (git-reference -- cgit v1.2.3 From 09b50a6ec25eadfdc60b7f77bb67816123c939df Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 16:08:47 +0200 Subject: gnu: bismark: Use git-file-name. * gnu/packages/bioinformatics.scm (bismark)[source]: Use git-file-name. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3ec0d0d301..92a765c688 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9179,7 +9179,7 @@ (define-public bismark (uri (git-reference (url "https://github.com/FelixKrueger/Bismark") (commit version))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 "0xchm3rgilj6vfjnyzfzzymfd7djr64sbrmrvs3njbwi66jqbzw9")))) -- cgit v1.2.3 From 3acfbd481117f217e03b596bd234c7b0da9cf18f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 16:09:07 +0200 Subject: gnu: f-seq: Use git-version and git-file-name. * gnu/packages/bioinformatics.scm (f-seq)[version]: Use git-version. [source]: Use git-file-name. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 92a765c688..c0f9c0768b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9115,13 +9115,13 @@ (define-public f-seq (revision "1")) (package (name "f-seq") - (version (string-append "1.1-" revision "." (string-take commit 7))) + (version (git-version "1.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/aboyle/F-seq") (commit commit))) - (file-name (string-append name "-" version)) + (file-name (git-file-name name version)) (sha256 (base32 "1nk33k0yajg2id4g59bc4szr58r2q6pdq42vgcw054m8ip9wv26h")) -- cgit v1.2.3 From 8c033085cc61365e7d685687b8d58bb0a2420663 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 16:09:35 +0200 Subject: gnu: r-chipkernels: Use git-version and git-file-name. * gnu/packages/bioinformatics.scm (r-chipkernels)[version]: Use git-version. [source]: Use git-file-name. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c0f9c0768b..f5a652832e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8080,14 +8080,14 @@ (define-public r-chipkernels (revision "1")) (package (name "r-chipkernels") - (version (string-append "1.1-" revision "." (string-take commit 9))) + (version (git-version "1.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/ManuSetty/ChIPKernels") (commit commit))) - (file-name (string-append name "-" version)) + (file-name (git-file-name name version)) (sha256 (base32 "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0")))) -- cgit v1.2.3 From d1e1c02e2850a0fd9c06c5884c7853d511948488 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 16:10:00 +0200 Subject: gnu: piranha: Use git-version. * gnu/packages/bioinformatics.scm (piranha)[version]: Use git-version. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f5a652832e..1adcc685e2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8258,7 +8258,7 @@ (define-public piranha (commit "0466d364b71117d01e4471b74c514436cc281233")) (package (name "piranha") - (version (string-append "1.2.1-" revision "." (string-take commit 9))) + (version (git-version "1.2.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference -- cgit v1.2.3 From f463f376e91ccc1fe4ab68d5e822b5d71a1234f5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 May 2021 16:10:20 +0200 Subject: gnu: bits: Use git-version and git-file-name. * gnu/packages/bioinformatics.scm (bits)[version]: Use git-version. [source]: Use git-file-name. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1adcc685e2..1f018befe6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8212,13 +8212,13 @@ (define-public bits (name "bits") ;; The version is 2.13.0 even though no release archives have been ;; published as yet. - (version (string-append "2.13.0-" revision "." (string-take commit 9))) + (version (git-version "2.13.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/arq5x/bits") (commit commit))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 "17n2kffk4kmhivd8c98g2vr6y1s23vbg4sxlxs689wni66797hbs")))) -- cgit v1.2.3 From 7ae2b1f2dcc35b1cb670cfa8c87b2d0a5779f5b9 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 1 Jun 2021 13:14:38 +0200 Subject: gnu: Add bamutils. * gnu/packages/bioinformatics.scm (bamutils): New variable. --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1f018befe6..66e790367d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -326,6 +326,37 @@ (define-public bamtools BAM files.") (license license:expat))) +(define-public bamutils + (package + (name "bamutils") + (version "1.0.13") + (source (origin + (method url-fetch) + (uri + (string-append + "https://genome.sph.umich.edu/w/images/7/70/" + "BamUtilLibStatGen." version ".tgz")) + (sha256 + (base32 + "0asr1kmjbr3cyf4hkg865y8c2s30v87xvws4q6c8pyfi6wfd1h8n")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests. + #:make-flags `("USER_WARNINGS=-std=gnu++98" + ,(string-append "INSTALLDIR=" + (assoc-ref %outputs "out") "/bin")) + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://genome.sph.umich.edu/wiki/BamUtil") + (synopsis "Programs for working on SAM/BAM files") + (description "This package provides several programs that perform +operations on SAM/BAM files. All of these programs are built into a +single executable called @code{bam}.") + (license license:gpl3+))) + (define-public bcftools (package (name "bcftools") -- cgit v1.2.3 From 18e0081045703f599aaf1789a206578a2854bdf2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 12:12:00 +0200 Subject: gnu: Add libmaus2. * gnu/packages/bioinformatics.scm (libmaus2): New variable. --- gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 66e790367d..ece59e982e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10969,6 +10969,46 @@ (define-public bandage (license (list license:gpl2+ ; bundled ogdf license:gpl3+)))) +(define-public libmaus2 + (package + (name "libmaus2") + (version "2.0.786") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/german.tischler/libmaus2") + (commit (string-append version "-release-20210531143054")))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1rxakmwjcx2yq5sjh3v849f7dfw4xzc2fyzf6s28s3p95z84w564")))) + (build-system gnu-build-system) + ;; The test suite attempts to execute ../test-driver, which does not exist. + (arguments '(#:tests? #false)) + (propagated-inputs + `(("zlib" ,zlib))) + (native-inputs + `(("gcc" ,gcc-10) ;Code has C++17 requirements + ("pkg-config" ,pkg-config))) + (home-page "https://gitlab.com/german.tischler/libmaus2") + (synopsis "Collection of data structures and algorithms useful for bioinformatics") + (description "libmaus2 is a collection of data structures and +algorithms. It contains: + +@itemize +@item I/O classes (single byte and UTF-8); +@item @code{bitio} classes (input, output and various forms of bit level + manipulation); +@item text indexing classes (suffix and LCP array, fulltext and minute (FM), + etc.); +@item BAM sequence alignment files input/output (simple and collating); +and many lower level support classes. +@end itemize\n") + ;; The code is explicitly available under the terms of either GPLv2 or + ;; GPLv3 according to the AUTHORS file, though most files have a GPLv3+ + ;; license header. + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-circus (package (name "r-circus") -- cgit v1.2.3 From 011d586c2c6c748fa203456d307d72447ed6b54e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jun 2021 13:45:54 +0200 Subject: gnu: Add biobambam2. * gnu/packages/bioinformatics.scm (biobambam2): New variable. --- gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ece59e982e..94d15cc4c0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11009,6 +11009,56 @@ (define-public libmaus2 ;; license header. (license (list license:gpl2+ license:gpl3+)))) +(define-public biobambam2 + (package + (name "biobambam2") + (version "2.0.182") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/german.tischler/biobambam2") + (commit (string-append version "-release-20210412001032")))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0b7w7a2a7hpkgrdn0n7hy4pilzrj82zqrh7q4bg1l0cd6bqr60m5")))) + (build-system gnu-build-system) + (arguments + ;; The test suite attempts to execute ../test-driver, which does not exist. + `(#:tests? #false + #:configure-flags + (list (string-append "--with-libmaus2=" + (assoc-ref %build-inputs "libmaus2"))))) + (inputs + `(("libmaus2" ,libmaus2) + ("xerces-c" ,xerces-c))) + (native-inputs + `(("gcc" ,gcc-10) ;Code has C++17 requirements + ("pkg-config" ,pkg-config))) + (home-page "https://gitlab.com/german.tischler/biobambam2") + (synopsis "Tools for processing BAM files") + (description "This package contains some tools for processing BAM files +including: + +@itemize +@item bamsormadup: parallel sorting and duplicate marking +@item bamcollate2: reads BAM and writes BAM reordered such that alignment or + collated by query name +@item bammarkduplicates: reads BAM and writes BAM with duplicate alignments + marked using the BAM flags field +@item bammaskflags: reads BAM and writes BAM while masking (removing) bits + from the flags column +@item bamrecompress: reads BAM and writes BAM with a defined compression + setting. This tool is capable of multi-threading. +@item bamsort: reads BAM and writes BAM resorted by coordinates or query name +@item bamtofastq: reads BAM and writes FastQ; output can be collated or + uncollated by query name. +@end itemize +") + ;; The COPYING file states that the code is distributed under version 3 of + ;; the GPL, but the license headers include the "or later" clause. + (license license:gpl3+))) + (define-public r-circus (package (name "r-circus") -- cgit v1.2.3 From 0928e552662965f5a18fbc831e6c9758744bd042 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Jun 2021 12:18:35 +0200 Subject: gnu: Add fit-sne. * gnu/packages/bioinformatics.scm (fit-sne): New variable. --- gnu/packages/bioinformatics.scm | 63 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 94d15cc4c0..408c93bd34 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11214,6 +11214,69 @@ (define-public find-circ in RNA-seq data.") (license license:gpl3)))) +(define-public fit-sne + (package + (name "fit-sne") + (version "1.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/KlugerLab/FIt-SNE") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1imq4577awc226wvygf94kpz156qdfw8xl0w0f7ss4w10lhmpmf5")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #false ; there are none + #:phases + ;; There is no build system. + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (invoke "g++" "-std=c++11" "-O3" + "src/sptree.cpp" + "src/tsne.cpp" + "src/nbodyfft.cpp" + "-o" "bin/fast_tsne" + "-pthread" "-lfftw3" "-lm" + "-Wno-address-of-packed-member"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (share (string-append out "/share/fit-sne"))) + (for-each (lambda (file) (install-file file bin)) + (find-files "bin")) + + (substitute* "fast_tsne.R" + (("^FAST_TSNE_SCRIPT_DIR.*") + (string-append "FAST_TSNE_SCRIPT_DIR = \"" out "\"\n"))) + (install-file "fast_tsne.R" share))))))) + (inputs + `(("fftw" ,fftw))) + (home-page "https://github.com/KlugerLab/FIt-SNE") + (synopsis "Fast Fourier Transform-accelerated interpolation-based t-SNE") + (description "@dfn{t-Stochastic Neighborhood Embedding} (t-SNE) is a +method for dimensionality reduction and visualization of high dimensional +datasets. A popular implementation of t-SNE uses the Barnes-Hut algorithm to +approximate the gradient at each iteration of gradient descent. This +implementation differs in these ways: + +@itemize +@item Instead of approximating the N-body simulation using Barnes-Hut, we + interpolate onto an equispaced grid and use FFT to perform the convolution. +@item Instead of computing nearest neighbors using vantage-point trees, we + approximate nearest neighbors using the Annoy library. The neighbor lookups + are multithreaded to take advantage of machines with multiple cores. +@end itemize +") + ;; See LICENSE.txt for details on what license applies to what files. + (license (list license:bsd-4 license:expat license:asl2.0)))) + (define-public python-scanpy (package (name "python-scanpy") -- cgit v1.2.3 From d06ae0580848f9fafdbd4337aef58f80b537d662 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 4 Jun 2021 12:55:28 +0200 Subject: gnu: Add pigx-sars-cov2-ww. * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable. --- gnu/packages/bioinformatics.scm | 48 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 408c93bd34..6cfe82fc90 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10633,6 +10633,54 @@ (define-public pigx-scrnaseq based methods.") (license license:gpl3+))) +(define-public pigx-sars-cov2-ww + (package + (name "pigx-sars-cov2-ww") + (version "0.0.1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BIMSBbioinfo/pigx_sarscov2_ww/" + "releases/download/v" version + "/pigx_sars-cov2-ww-" version ".tar.gz")) + (sha256 + (base32 + "1h1rfl3dyf7pid74xxgiyr4x1l5yj000wcz5crm1bdbaz8p7b7ic")))) + (build-system gnu-build-system) + (inputs + `(("bash-minimal" ,bash-minimal) + ("bwa" ,bwa) + ("ensembl-vep" ,ensembl-vep) + ("fastqc" ,fastqc) + ("kraken2" ,kraken2) + ("krona-tools" ,krona-tools) + ("lofreq" ,lofreq) + ("multiqc" ,multiqc) + ("prinseq" ,prinseq) + ("python-pyyaml" ,python-pyyaml) + ("python-wrapper" ,python-wrapper) + ("r-base64url" ,r-base64url) + ("r-dplyr" ,r-dplyr) + ("r-dt" ,r-dt) + ("r-ggplot2" ,r-ggplot2) + ("r-magrittr" ,r-magrittr) + ("r-minimal" ,r-minimal) + ("r-plotly" ,r-plotly) + ("r-qpcr" ,r-qpcr) + ("r-reshape2" ,r-reshape2) + ("r-rmarkdown" ,r-rmarkdown) + ("r-stringr" ,r-stringr) + ("r-tidyr" ,r-tidyr) + ("samtools" ,samtools) + ("snakemake" ,snakemake))) + (home-page "https://bioinformatics.mdc-berlin.de/pigx/") + (synopsis "Analysis pipeline for wastewater sequencing") + (description "PiGx SARS-CoV-2 is a pipeline for analysing data from +sequenced wastewater samples and identifying given variants-of-concern of +SARS-CoV-2. The pipeline can be used for continuous sampling. The output +report will provide an intuitive visual overview about the development of +variant abundance over time and location.") + (license license:gpl3+))) + (define-public pigx (package (name "pigx") -- cgit v1.2.3 From 7382aa00b82860762bc326dec6b45f8cd2161327 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 1 Jun 2021 10:25:12 +0200 Subject: gnu: python-scanpy: Update to 1.7.2. * gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2. --- gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++---- 1 file changed, 21 insertions(+), 4 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6cfe82fc90..c1cfabc27f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -122,6 +122,7 @@ (define-module (gnu packages bioinformatics) #:use-module (gnu packages popt) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) + #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) #:use-module (gnu packages python-compression) #:use-module (gnu packages python-science) @@ -11328,14 +11329,14 @@ (define-public fit-sne (define-public python-scanpy (package (name "python-scanpy") - (version "1.4.6") + (version "1.7.2") (source (origin (method url-fetch) (uri (pypi-uri "scanpy" version)) (sha256 (base32 - "0s2b6cvaigx4wzw3850qb93sjwwxbzh22kpbp498zklc5rjpbz4l")))) + "0c66adnfizsyk0h8bv2yhmay876z0klpxwpn4z6m71wly7yplpmd")))) (build-system python-build-system) (arguments `(#:phases @@ -11346,12 +11347,25 @@ (define-public python-scanpy (delete-file-recursively "scanpy/tests/notebooks") (delete-file "scanpy/tests/test_clustering.py") (delete-file "scanpy/tests/test_datasets.py") + (delete-file "scanpy/tests/test_highly_variable_genes.py") ;; TODO: I can't get the plotting tests to work, even with Xvfb. (delete-file "scanpy/tests/test_plotting.py") (delete-file "scanpy/tests/test_preprocessing.py") (delete-file "scanpy/tests/test_read_10x.py") + ;; The following tests need anndata.tests, which aren't included + ;; in the final python-anndata package. + (delete-file "scanpy/tests/test_combat.py") + (delete-file "scanpy/tests/test_embedding_plots.py") + (delete-file "scanpy/tests/test_normalization.py") + (delete-file "scanpy/tests/test_pca.py") + (delete-file "scanpy/tests/external/test_scrublet.py") + + ;; The following tests requires 'scanorama', which isn't + ;; packaged yet. + (delete-file "scanpy/tests/external/test_scanorama_integrate.py") + (setenv "PYTHONPATH" (string-append (getcwd) ":" (getenv "PYTHONPATH"))) @@ -11376,11 +11390,14 @@ (define-public python-scanpy ("python-seaborn" ,python-seaborn) ("python-statsmodels" ,python-statsmodels) ("python-tables" ,python-tables) + ("python-pytoml" ,python-pytoml) ("python-tqdm" ,python-tqdm) ("python-umap-learn" ,python-umap-learn))) (native-inputs - `(("python-pytest" ,python-pytest) - ("python-setuptools-scm" ,python-setuptools-scm))) + `(("python-leidenalg" ,python-leidenalg) + ("python-pytest" ,python-pytest) + ("python-setuptools-scm" ,python-setuptools-scm) + ("python-sinfo" ,python-sinfo))) (home-page "https://github.com/theislab/scanpy") (synopsis "Single-Cell Analysis in Python.") (description "Scanpy is a scalable toolkit for analyzing single-cell gene -- cgit v1.2.3 From f98837a6baca957098d073d5bb8d440ddf9ffefb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 5 Jun 2021 00:33:00 +0200 Subject: gnu: pigx-rnaseq: Update to 0.0.13. * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.13. [arguments]: Remove obsolete substitutions. [inputs]: Remove fastqc and trim-galore; add hisat2 and fastp. --- gnu/packages/bioinformatics.scm | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c1cfabc27f..dab097381a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10355,7 +10355,7 @@ (define-public dropseq-tools (define-public pigx-rnaseq (package (name "pigx-rnaseq") - (version "0.0.10") + (version "0.0.13") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" @@ -10363,7 +10363,7 @@ (define-public pigx-rnaseq "/pigx_rnaseq-" version ".tar.gz")) (sha256 (base32 - "0z3hr120wk2vrlmlpz1vp3n9wy3rq4y2mnzh2vf08qgqn2xfdwcw")))) + "0z9zid2c8q16lfzlnjd63nparknhv31qgv4h79algmvhkakm2pgk")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f ; not supported @@ -10373,19 +10373,17 @@ (define-public pigx-rnaseq (add-after 'unpack 'disable-resource-intensive-test (lambda _ (substitute* "Makefile.in" - (("(^ tests/test_trim_galore/test.sh).*" _ m) m) (("^ tests/test_multiqc/test.sh") "") - (("^ test.sh") "")) - #t))))) + (("^ test.sh") ""))))))) (inputs `(("coreutils" ,coreutils) ("sed" ,sed) ("gzip" ,gzip) ("snakemake" ,snakemake) - ("fastqc" ,fastqc) ("multiqc" ,multiqc) ("star" ,star-for-pigx) - ("trim-galore" ,trim-galore) + ("hisat2" ,hisat2) + ("fastp" ,fastp) ("htseq" ,htseq) ("samtools" ,samtools) ("r-minimal" ,r-minimal) -- cgit v1.2.3 From d1e7b50dbf58c59c100f1bf5a7ea735daa3a203f Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Sun, 6 Jun 2021 02:06:51 +0200 Subject: gnu: python-cooler: Update to 0.8.11. * gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.11. [arguments]: Add build phase "patch-tests"; replace "check" phase. [native-inputs]: Add python-codecov, python-pytest-cov, and python-pytest-flake8. [propagated-inputs]: Add python-six and python-sparse. --- gnu/packages/bioinformatics.scm | 42 +++++++++++++++++++++++++++++++++++------ 1 file changed, 36 insertions(+), 6 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dab097381a..2de8a59d3c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11717,15 +11717,39 @@ (define-public python2-pyfaidx (define-public python-cooler (package (name "python-cooler") - (version "0.8.7") + (version "0.8.11") (source (origin (method url-fetch) (uri (pypi-uri "cooler" version)) (sha256 (base32 - "01g6gqix9ba27sappz6nfyiwabzrlf8i5fn8kwcz8ra356cq9crp")))) + "1i96fmpsimj4wrx51rxn8lw2gqxf5a2pvrj5rwdd6ivnm3pmhyrn")))) (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-tests + (lambda _ + (substitute* "tests/test_create.py" + (("def test_roundtrip") + (string-append "@pytest.mark.skip(reason=\"requires network " + "access to genome.ucsc.edu\")\n" + "def test_roundtrip"))) + (substitute* "tests/test_util.py" + (("def test_fetch_chromsizes") + (string-append "@pytest.mark.skip(reason=\"requires network " + "access to genome.ucsc.edu\")\n" + "def test_fetch_chromsizes"))) + ;; This test depends on ipytree, which contains a lot of minified + ;; JavaScript. + (substitute* "tests/test_fileops.py" + (("def test_print_trees") + "def _test_print_trees")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "pytest" "-v"))))))) (propagated-inputs `(("python-asciitree" ,python-asciitree) ("python-biopython" ,python-biopython) @@ -11741,11 +11765,17 @@ (define-public python-cooler ("python-pysam" ,python-pysam) ("python-pyyaml" ,python-pyyaml) ("python-scipy" ,python-scipy) - ("python-simplejson" ,python-simplejson))) + ("python-simplejson" ,python-simplejson) + ("python-six" ,python-six) + ("python-sparse" ,python-sparse))) (native-inputs - `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest))) - (home-page "https://github.com/mirnylab/cooler") + `(("python-codecov" ,python-codecov) + ("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-flake8" ,python-pytest-flake8))) + ;; Almost all the projects of the Mirnylab are moved under Open2C umbrella + (home-page "https://github.com/open2c/cooler") (synopsis "Sparse binary format for genomic interaction matrices") (description "Cooler is a support library for a sparse, compressed, binary persistent -- cgit v1.2.3 From b65c02e2d35af6fbe1d1810d6c69cfab194e13e2 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 6 Jun 2021 12:07:01 +0300 Subject: gnu: freebayes: Update to 1.3.5. * gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.5. [source]: Remove patch. [arguments]: Adjust custom 'patch-source phase for changes in source. [inputs]: Remove zlib. * gnu/packages/patches/freebayes-devendor-deps.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 16 +-- gnu/packages/patches/freebayes-devendor-deps.patch | 152 --------------------- 3 files changed, 7 insertions(+), 162 deletions(-) delete mode 100644 gnu/packages/patches/freebayes-devendor-deps.patch (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/local.mk b/gnu/local.mk index 1c692e0ce4..153f6ee8d7 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1019,7 +1019,6 @@ dist_patch_DATA = \ %D%/packages/patches/fpc-reproducibility.patch \ %D%/packages/patches/fplll-std-fenv.patch \ %D%/packages/patches/freedink-engine-fix-sdl-hints.patch \ - %D%/packages/patches/freebayes-devendor-deps.patch \ %D%/packages/patches/freeimage-unbundle.patch \ %D%/packages/patches/fuse-overlapping-headers.patch \ %D%/packages/patches/gajim-honour-GAJIM_PLUGIN_PATH.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2de8a59d3c..1e38c6e0e7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13572,7 +13572,7 @@ (define-public vcflib (define-public freebayes (package (name "freebayes") - (version "1.3.3") + (version "1.3.5") (source (origin (method git-fetch) (uri (git-reference @@ -13580,8 +13580,7 @@ (define-public freebayes (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0myz3giad7jqp6ricdfnig9ymlcps2h67mlivadvx97ngagm85z8")) - (patches (search-patches "freebayes-devendor-deps.patch")) + (base32 "1l0z88gq57kva677a6xri5g9k2d9h9lk5yk1q2xmq64wqhv7dvc3")) (modules '((guix build utils))) (snippet '(begin @@ -13593,8 +13592,7 @@ (define-public freebayes ("htslib" ,htslib) ("smithwaterman" ,smithwaterman) ("tabixpp" ,tabixpp) - ("vcflib" ,vcflib) - ("zlib" ,zlib))) + ("vcflib" ,vcflib))) (native-inputs `(("bash-tap" ,bash-tap) ("bc" ,bc) @@ -13627,13 +13625,13 @@ (define-public freebayes (string-append bash-tap "/bin/bash-tap-bootstrap")) (("source.*bash-tap-bootstrap") (string-append "source " bash-tap "/bin/bash-tap-bootstrap"))) - (substitute* "meson.build" - ;; Some inputs aren't actually needed. - ((".*bamtools/src.*") "") - ((".*multichoose.*") "")) (substitute* '("src/BedReader.cpp" "src/BedReader.h") (("../intervaltree/IntervalTree.h") "IntervalTree.h")) + (substitute* "meson.build" + ;; Our pkg-config file is vcflib.pc + (("libvcflib") "vcflib") + (("vcflib_inc,") "")) #t))) (add-after 'unpack 'unpack-submodule-sources (lambda* (#:key inputs #:allow-other-keys) diff --git a/gnu/packages/patches/freebayes-devendor-deps.patch b/gnu/packages/patches/freebayes-devendor-deps.patch deleted file mode 100644 index 9886de11fb..0000000000 --- a/gnu/packages/patches/freebayes-devendor-deps.patch +++ /dev/null @@ -1,152 +0,0 @@ -This patch is original to Guix, ongoing work to upstream bits as possible. - -From 9acc56db5e7469f5976be38b52ba4993de98ee38 Mon Sep 17 00:00:00 2001 -From: Efraim Flashner -Date: Sun, 17 Jan 2021 13:27:17 +0200 -Subject: [PATCH] devendor-dependants - ---- - meson.build | 84 +++++++++++++++++++++++++++++++++++++++++------------ - 1 file changed, 66 insertions(+), 18 deletions(-) - -diff --git a/meson.build b/meson.build -index f6bf242..bded4af 100644 ---- a/meson.build -+++ b/meson.build -@@ -9,8 +9,13 @@ project('freebayes', ['cpp', 'c'], - - zlib_dep = dependency('zlib') - lzma_dep = dependency('liblzma') -+simde_dep = dependency('simde') - bzip2_dep = dependency('bz2lib', required: false) - htslib_dep = dependency('htslib', required : false) -+tabixpp_dep = dependency('tabixpp', required : false) -+fastahack_dep = dependency('fastahack', required : false) -+smithwaterman_dep = dependency('smithwaterman', required : false) -+vcflib_dep = dependency('vcflib', required: false) - thread_dep = dependency('threads') - - if htslib_dep.found() -@@ -59,6 +64,56 @@ else - ] - endif - -+if tabixpp_dep.found() -+ tabixpp_includes = '' -+ tabixpp_src = [] -+else -+ tabixpp_includes = [ -+ 'vcflib/tabixpp', -+ ] -+ tabixpp_src = [ -+ 'vcflib/tabixpp/tabix.cpp', -+ ] -+endif -+ -+if vcflib_dep.found() -+ vcflib_includes = '' -+ vcflib_src = [] -+else -+ vcflib_includes = [ -+ 'vcflib/src', -+ 'vcflib/multichoose', -+ 'vcflib/filevercmp', -+ ] -+ vcflib_src = [ -+ 'vcflib/src/Variant.cpp', -+ ] -+endif -+ -+if fastahack_dep.found() -+ fastahack_src = [] -+else -+ fastahack_src = [ -+ 'vcflib/fastahack/Fasta.cpp', -+ 'vcflib/src/split.cpp', -+ ] -+endif -+ -+if smithwaterman_dep.found() -+ smithwaterman_includes = '' -+ smithwaterman_src = [] -+else -+ smithwaterman_includes = [ -+ 'vcflib/smithwaterman', -+ ] -+ smithwaterman_src = [ -+ 'vcflib/smithwaterman/SmithWatermanGotoh.cpp', -+ 'vcflib/smithwaterman/disorder.cpp', -+ 'vcflib/smithwaterman/Repeats.cpp', -+ 'vcflib/smithwaterman/LeftAlign.cpp', -+ 'vcflib/smithwaterman/IndelAllele.cpp', -+ ] -+endif - - - # -@@ -105,23 +160,18 @@ seqlib_src = [ - ] - - vcflib_src = [ -- 'vcflib/tabixpp/tabix.cpp', -- 'vcflib/src/Variant.cpp', -- 'vcflib/smithwaterman/SmithWatermanGotoh.cpp', -- 'vcflib/smithwaterman/disorder.cpp', -- 'vcflib/smithwaterman/Repeats.cpp', -- 'vcflib/smithwaterman/LeftAlign.cpp', -- 'vcflib/smithwaterman/IndelAllele.cpp', -+ vcflib_src, -+ tabixpp_src, -+ smithwaterman_src, - ] - - bamleftalign_src = [ - 'src/bamleftalign.cpp', - 'src/IndelAllele.cpp', - 'contrib/SeqLib/src/BamWriter.cpp', -- 'vcflib/fastahack/Fasta.cpp', -- 'vcflib/smithwaterman/LeftAlign.cpp', -- 'vcflib/smithwaterman/IndelAllele.cpp', -- 'vcflib/src/split.cpp', -+ fastahack_src, -+ smithwaterman_src, -+ vcflib_src, - 'src/LeftAlign.cpp', - ] - -@@ -134,11 +184,9 @@ incdir = include_directories( - 'ttmath', - 'contrib', - 'contrib/SeqLib', -- 'vcflib/src', -- 'vcflib/tabixpp', -- 'vcflib/smithwaterman', -- 'vcflib/multichoose', -- 'vcflib/filevercmp') -+ tabixpp_includes, -+ smithwaterman_includes, -+ vcflib_includes) - - c_args = ['-fpermissive','-w'] - cpp_args = ['-fpermissive','-w','-Wc++14-compat'] -@@ -152,7 +200,7 @@ executable('freebayes', - include_directories : incdir, - cpp_args : cpp_args, - c_args : c_args, -- dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep], -+ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, smithwaterman_dep, vcflib_dep, thread_dep], - install: true - ) - -@@ -165,7 +213,7 @@ executable('bamleftalign', - include_directories : incdir, - cpp_args : cpp_args, - c_args : c_args, -- dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep], -+ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, fastahack_dep, smithwaterman_dep, vcflib_dep, thread_dep], - install: true - ) - --- -2.30.0 - -- cgit v1.2.3