From bc70516bbae8a6388f3ed19008d3e10efd1577a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 14 Jun 2019 17:26:27 +0200 Subject: gnu: Remove r-loomr. The loomR package is actually non-free software according to its author. See https://github.com/mojaveazure/loomR/pull/24. * gnu/packages/bioinformatics.scm (r-loomr): Remove variable. --- gnu/packages/bioinformatics.scm | 29 ----------------------------- 1 file changed, 29 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8dbcd5dd33..b950b8cf53 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13086,35 +13086,6 @@ (define-public r-circus can be calculated, and a number of descriptive plots easily generated.") (license license:artistic2.0))) -(define-public r-loomr - (let ((commit "df0144bd2bbceca6fadef9edc1bbc5ca672d4739") - (revision "1")) - (package - (name "r-loomr") - (version (git-version "0.2.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/mojaveazure/loomR.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1b1g4dlmfdyhn56bz1mkh9ymirri43wiz7rjhs7py3y7bdw1s3yr")))) - (build-system r-build-system) - (propagated-inputs - `(("r-r6" ,r-r6) - ("r-hdf5r" ,r-hdf5r) - ("r-iterators" ,r-iterators) - ("r-itertools" ,r-itertools) - ("r-matrix" ,r-matrix))) - (home-page "https://github.com/mojaveazure/loomR") - (synopsis "R interface for loom files") - (description "This package provides an R interface to access, create, -and modify loom files. loomR aims to be completely compatible with loompy.") - (license license:gpl3)))) - (define-public gffread ;; We cannot use the tagged release because it is not in sync with gclib. ;; See https://github.com/gpertea/gffread/issues/26 -- cgit v1.2.3 From 7bbd06ed597b0035aa0f12782e7af9b603253aaa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:54:51 +0200 Subject: gnu: r-systempiper: Update to 1.18.1. * gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.18.1. --- 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 b950b8cf53..fa0e610433 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6946,14 +6946,14 @@ (define-public r-shortread (define-public r-systempiper (package (name "r-systempiper") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "1063vdf4g2i5xyabwvzkqfxd2j8s4zs6z4zxf8lx2ccjddhkn37a")))) + "1k57zyzagd7g7wl38l3cn9csylykxcllbfvyq7dz8pvihgkn0ssi")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 6dc3c5872893845935f958b260f063166dd2cae4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:54:56 +0200 Subject: gnu: r-tximport: Update to 1.12.1. * gnu/packages/bioinformatics.scm (r-tximport): Update to 1.12.1. --- 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 fa0e610433..6a66e60cf0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8548,13 +8548,13 @@ (define-public r-seqgl (define-public r-tximport (package (name "r-tximport") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "0nl4imr5klwcd0xnp5y0g61d6mcgd50q60zkl86ymfmc0id368jr")))) + "1nq8v1sgkm2ssmvr2z3qw0zsk7zy0dzb95g1mfs8fkpjqh3nqq5s")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") -- cgit v1.2.3 From 42df44f6454ff7a597493def6f57718b1b338c3d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 04:55:03 +0200 Subject: gnu: r-seurat: Update to 3.0.2. * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.0.2. --- 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 6a66e60cf0..90f12f41ec 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9452,13 +9452,13 @@ (define-public r-msnid (define-public r-seurat (package (name "r-seurat") - (version "3.0.1") + (version "3.0.2") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "0mx2fvhdswbcsgqxhfc6d0gr92bkibwpz2bavqdzbbxrzpdpnilc")))) + "016fgcmjz3sjfxdvam5hd7mdxpmpnc7f6p5zqlh97m21dgn5vpqn")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a6f2ced34b873612e6caca719ed448af3ee92b7e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 17 Jun 2019 14:39:29 +0200 Subject: gnu: Add tbsp. * gnu/packages/bioinformatics.scm (tbsp): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 90f12f41ec..8002f24110 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14756,3 +14756,40 @@ (define-public r-psiplot vast-tools, an RNA-Seq pipeline for alternative splicing analysis. The plots are generated using @code{ggplot2}.") (license license:expat))) + +(define-public tbsp + (let ((commit "ec8fff4410cfb13a677dbbb95cbbc60217e64907") + (revision "1")) + (package + (name "tbsp") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/phoenixding/tbsp.git") + (commit commit))) + (sha256 + (base32 + "025ym14x8gbd6hb55lsinqj6f5qzw36i10klgs7ldzxxd7s39ki1")))) + (build-system python-build-system) + (arguments '(#:tests? #f)) ; no tests included + (inputs + `(("python-matplotlib" ,python-matplotlib) + ("python-networkx" ,python-networkx) + ("python-numpy" ,python-numpy) + ("python-pybigwig" ,python-pybigwig) + ("python-biopython" ,python-biopython) + ("python-scikit-learn" ,python-scikit-learn) + ("python-scipy" ,python-scipy))) + (home-page "https://github.com/phoenixding/tbsp/") + (synopsis "SNP-based trajectory inference") + (description + "Several studies focus on the inference of developmental and response +trajectories from single cell RNA-Seq (scRNA-Seq) data. A number of +computational methods, often referred to as pseudo-time ordering, have been +developed for this task. CRISPR has also been used to reconstruct lineage +trees by inserting random mutations. The tbsp package implements an +alternative method to detect significant, cell type specific sequence +mutations from scRNA-Seq data.") + (license license:expat)))) -- cgit v1.2.3 From 7cb44fb5718c748a80e05a673f9b5faaa7586137 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 20 Jun 2019 14:02:27 +0200 Subject: gnu: ncbi-vdb: Update to 2.9.6. * gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.6. [arguments]: Pass HAVE_HDF5 make flag; add build phase "patch-krypto-flags". --- gnu/packages/bioinformatics.scm | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8002f24110..2862cb1187 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5582,7 +5582,7 @@ (define-public java-ngs (define-public ncbi-vdb (package (name "ncbi-vdb") - (version "2.9.3") + (version "2.9.6") (source (origin (method git-fetch) (uri (git-reference @@ -5591,11 +5591,12 @@ (define-public ncbi-vdb (file-name (git-file-name name version)) (sha256 (base32 - "1l4ny67nxwv1lagk9wwjbrgm7ln7adci6dnpc7k1yaln6shj0qpm")))) + "0knkj1sq34hlivgv5qd6jlczqrs3ldmfgn6vbbw7p4mqxvb9mirk")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported #:tests? #f ; no "check" target + #:make-flags '("HAVE_HDF5=1") #:phases (modify-phases %standard-phases (add-after 'unpack 'make-files-writable @@ -5607,6 +5608,13 @@ (define-public ncbi-vdb (string-append (getcwd) "/setup:" (getenv "PERL5LIB"))) #t)) + ;; See https://github.com/ncbi/ncbi-vdb/issues/14 + (add-after 'unpack 'patch-krypto-flags + (lambda _ + (substitute* "libs/krypto/Makefile" + (("-Wa,-march=generic64\\+aes") "") + (("-Wa,-march=generic64\\+sse4") "")) + #t)) (replace 'configure (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) -- cgit v1.2.3 From 20874b7044ec3ee28dc8302dc79e3623f6aae53b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 20 Jun 2019 14:30:24 +0200 Subject: gnu: sra-tools: Update to 2.9.6. * gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.6. --- 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 2862cb1187..c30b12dfab 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5941,7 +5941,7 @@ (define-public python2-screed (define-public sra-tools (package (name "sra-tools") - (version "2.9.3") + (version "2.9.6") (source (origin (method git-fetch) @@ -5951,7 +5951,7 @@ (define-public sra-tools (file-name (git-file-name name version)) (sha256 (base32 - "0663gcdxkziwsmlznjxysb00621rllpbz6jwsfifq7z3dj3lwm8b")))) + "0vqzap68v81k0zif2mnqfy8pnw2nrhsg87p6mgq8qk3nk2jv2rgy")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported -- cgit v1.2.3 From 30adfd36007884695d792eb78886d42e69266270 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 20 Jun 2019 14:33:45 +0200 Subject: gnu: ngs-sdk: Update to 2.9.6. * gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.6. --- 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 c30b12dfab..8cbb2e10d0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5516,7 +5516,7 @@ (define-public mosaik (define-public ngs-sdk (package (name "ngs-sdk") - (version "2.9.3") + (version "2.9.6") (source (origin (method git-fetch) (uri (git-reference @@ -5525,7 +5525,7 @@ (define-public ngs-sdk (file-name (git-file-name name version)) (sha256 (base32 - "17c0v1nah3g3d2ib5bbi0vhma1ghd6vb9xycavqsh64lhp840rk3")))) + "0d5k5kabgl15as37kj9x65xc92j4gcqms86hvihw3yb6wag0r0q3")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported -- cgit v1.2.3 From 28618b05f002720bc56bae76659717a0eba4dd8b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 20 Jun 2019 22:29:07 +0200 Subject: gnu: pigx-rnaseq: Update to 0.0.7. * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.7. [inputs]: Add coreutils and sed. --- gnu/packages/bioinformatics.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8cbb2e10d0..f1a73bca7e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12544,15 +12544,15 @@ (define-public dropseq-tools (define-public pigx-rnaseq (package (name "pigx-rnaseq") - (version "0.0.6") + (version "0.0.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" - "releases/download/v." version + "releases/download/v" version "/pigx_rnaseq-" version ".tar.gz")) (sha256 (base32 - "1w7cwbbz1sbvbyqh5c60iqcjfs3qsppmdgxqa1i0w5wwb9mkh27m")))) + "013inbh22bjvwg2w0kx5i42k66w1zl4310ldip2ax6msgprs2ydj")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f ; not supported @@ -12567,7 +12567,9 @@ (define-public pigx-rnaseq (("^ test.sh") "")) #t))))) (inputs - `(("gzip" ,gzip) + `(("coreutils" ,coreutils) + ("sed" ,sed) + ("gzip" ,gzip) ("snakemake" ,snakemake) ("fastqc" ,fastqc) ("multiqc" ,multiqc) -- cgit v1.2.3