From 6e54ce9ca9b172189ab46eb14147304ff9cfa35b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 1 Jun 2022 12:18:00 +0200 Subject: gnu: pigx-chipseq: Update to 0.1.0. * gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.1.0. [source]: Remove patch. [arguments]: Remove 'autoreconf phase. [native-inputs]: Remove autoconf and automake. * gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove patch. --- gnu/packages/bioinformatics.scm | 19 +++---------------- 1 file changed, 3 insertions(+), 16 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1ffac1a0ca..f2800d3163 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10526,7 +10526,7 @@ (define-public pigx-rnaseq (define-public pigx-chipseq (package (name "pigx-chipseq") - (version "0.0.53") + (version "0.1.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" @@ -10534,25 +10534,12 @@ (define-public pigx-chipseq "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "0c6npx35sszycf059w1x1k4k9hq1qqxny0i4p57q1188czr4561h")) - (patches (search-patches "pigx-chipseq-no-citeproc.patch")))) + "008n6drj9q5av86xihxlj4py2c9p3c5z5ld89c3bksrp77zxiy67")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; parts of the tests rely on access to the network #:phases (modify-phases %standard-phases - (add-before 'bootstrap 'autoreconf - (lambda _ - ;; This was fixed in commit - ;; 0b1c9f7f2e4d0ff601f1de95ab8b2953f4d5dbc7, but there is no - ;; release with this fix. - (call-with-output-file "VERSION" - (lambda (port) (display ,version port))) - ;; See https://github.com/BIMSBbioinfo/pigx_chipseq/issues/176 - (substitute* "m4/ax_r_package.m4" - (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)") - "if(system.file(package=\"PKG\") == \"\")")) - (invoke "autoreconf" "-vif"))) (add-before 'configure 'set-PYTHONPATH (lambda _ (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) @@ -10606,7 +10593,7 @@ (define-public pigx-chipseq bedtools kentutils)) (native-inputs - (list autoconf automake python-pytest)) + (list python-pytest)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for ChIP sequencing experiments") (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak -- cgit v1.2.3 From 93c97bfffba7ca0126c03967fbe058354e24f84d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 1 Jun 2022 12:41:59 +0200 Subject: gnu: pigx-bsseq: Update to 0.1.7. * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.7. [source]: Remove patch. [arguments]: Remove 'autoreconf phase. [native-inputs]: Remove automake and autoconf. * gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove patch. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 19 +++---------- gnu/packages/patches/pigx-bsseq-no-citeproc.patch | 33 ----------------------- 3 files changed, 3 insertions(+), 50 deletions(-) delete mode 100644 gnu/packages/patches/pigx-bsseq-no-citeproc.patch (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/local.mk b/gnu/local.mk index b9d62a3f0f..c7625a7679 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1628,7 +1628,6 @@ dist_patch_DATA = \ %D%/packages/patches/picard-fix-id3-rename-test.patch \ %D%/packages/patches/picprog-non-intel-support.patch \ %D%/packages/patches/pidgin-add-search-path.patch \ - %D%/packages/patches/pigx-bsseq-no-citeproc.patch \ %D%/packages/patches/pinball-system-ltdl.patch \ %D%/packages/patches/pingus-boost-headers.patch \ %D%/packages/patches/pingus-sdl-libs-config.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f2800d3163..92d92e7d02 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10608,7 +10608,7 @@ (define-public pigx-chipseq (define-public pigx-bsseq (package (name "pigx-bsseq") - (version "0.1.6") + (version "0.1.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/" @@ -10616,8 +10616,7 @@ (define-public pigx-bsseq "/pigx_bsseq-" version ".tar.gz")) (sha256 (base32 - "1dipikph0xdr8fp0h1flpafcrg60y4aabljg8fl1v92j3gxdggmw")) - (patches (search-patches "pigx-bsseq-no-citeproc.patch")))) + "1hfiignq3410dbl6f67vc6zr69abknpcgxixx475dspky2jb5lyn")))) (build-system gnu-build-system) (arguments `(;; TODO: tests currently require 12+GB of RAM. See @@ -10625,18 +10624,6 @@ (define-public pigx-bsseq #:tests? #f #:phases (modify-phases %standard-phases - (add-before 'bootstrap 'autoreconf - (lambda _ - ;; This was fixed in commit - ;; d56ac732524da659afbbb0972f7a87fa178ae58e, but there is no - ;; release with this fix. - (call-with-output-file "VERSION" - (lambda (port) (display ,version port))) - ;; https://github.com/BIMSBbioinfo/pigx_bsseq/issues/181 - (substitute* "m4/ax_r_package.m4" - (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)") - "if(system.file(package=\"PKG\") == \"\")")) - (invoke "autoreconf" "-vif"))) (add-before 'configure 'set-PYTHONPATH (lambda _ (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))) @@ -10648,7 +10635,7 @@ (define-public pigx-bsseq (search-input-directory inputs "share/zoneinfo"))))))) (native-inputs - (list tzdata automake autoconf)) + (list tzdata)) (inputs (list coreutils sed diff --git a/gnu/packages/patches/pigx-bsseq-no-citeproc.patch b/gnu/packages/patches/pigx-bsseq-no-citeproc.patch deleted file mode 100644 index 882e660fe4..0000000000 --- a/gnu/packages/patches/pigx-bsseq-no-citeproc.patch +++ /dev/null @@ -1,33 +0,0 @@ -diff -Naur pigx_bsseq-0.1.5/configure.ac pigx_bsseq-0.1.5.patched/configure.ac ---- pigx_bsseq-0.1.5/configure.ac 2021-06-08 15:28:08.000000000 +0200 -+++ pigx_bsseq-0.1.5.patched/configure.ac 2021-10-05 14:43:56.806529137 +0200 -@@ -38,7 +38,6 @@ - find_or_override_prog([GNUBASH], [bash]) - find_or_override_prog([SNAKEMAKE], [snakemake]) - find_or_override_prog([PANDOC], [pandoc]) --find_or_override_prog([PANDOC_CITEPROC], [pandoc-citeproc]) - find_or_override_prog([FASTQC], [fastqc]) - find_or_override_prog([MULTIQC], [multiqc]) - find_or_override_prog([TRIMGALORE], [trim_galore]) -diff -Naur pigx_bsseq-0.1.5/Makefile.in pigx_bsseq-0.1.5.patched/Makefile.in ---- pigx_bsseq-0.1.5/Makefile.in 2021-06-08 16:17:03.000000000 +0200 -+++ pigx_bsseq-0.1.5.patched/Makefile.in 2021-10-05 14:43:34.635876855 +0200 -@@ -408,7 +408,6 @@ - PACKAGE_URL = @PACKAGE_URL@ - PACKAGE_VERSION = @PACKAGE_VERSION@ - PANDOC = @PANDOC@ --PANDOC_CITEPROC = @PANDOC_CITEPROC@ - PATH_SEPARATOR = @PATH_SEPARATOR@ - PYTHON = @PYTHON@ - PYTHONPATH = @PYTHONPATH@ -diff -Naur pigx_bsseq-0.1.5/pigx-common/common/pigx-runner.in pigx_bsseq-0.1.5.patched/pigx-common/common/pigx-runner.in ---- pigx_bsseq-0.1.5/pigx-common/common/pigx-runner.in 2021-06-08 10:14:29.000000000 +0200 -+++ pigx_bsseq-0.1.5.patched/pigx-common/common/pigx-runner.in 2021-10-05 14:43:44.296161069 +0200 -@@ -375,7 +375,6 @@ - if path.exists(bin): shutil.rmtree(bin) - os.makedirs(bin, exist_ok=True) - os.symlink('@PANDOC@', path.join(bin, "pandoc")) -- os.symlink('@PANDOC_CITEPROC@', path.join(bin, "pandoc-citeproc")) - os.symlink('@RSCRIPT@', path.join(bin, "Rscript")) - os.environ['PATH'] = path.abspath(bin) + ":" + os.environ['PATH'] - os.environ['PIGX_PATH'] = path.abspath(bin) + ":" + os.environ['PATH'] -- cgit v1.2.3 From b540e5e6bba6e0047864abcc3a6dfec46ff6cd32 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 1 Jun 2022 12:57:22 +0200 Subject: gnu: pigx-scrnaseq: Update to 1.1.9. * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.9. [arguments]: Remove 'autoreconf phase. [native-inputs]: Remove autoconf and automake. --- gnu/packages/bioinformatics.scm | 18 ++---------------- 1 file changed, 2 insertions(+), 16 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 92d92e7d02..931eea7022 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10679,7 +10679,7 @@ (define-public pigx-bsseq (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "1.1.8") + (version "1.1.9") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -10687,23 +10687,11 @@ (define-public pigx-scrnaseq "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "1lc42hl8mz95kilh0z39s3wnv092mhm6vl2i394n0yfvdzk4f885")))) + "0adx7877c3lhlrzfid76i8bc829wcmzvrm0jx47gyid8mxqb7vqs")))) (build-system gnu-build-system) (arguments `(#:phases (modify-phases %standard-phases - (add-before 'bootstrap 'autoreconf - (lambda _ - ;; This was fixed in commit - ;; c4ac067438ae9312b5786a72e2bfb3d795e3ec8a, but there is no - ;; release with this fix. - (call-with-output-file "VERSION" - (lambda (port) (display ,version port))) - ;; https://github.com/BIMSBbioinfo/pigx_scrnaseq/issues/59 - (substitute* "m4/ax_r_package.m4" - (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)") - "if(system.file(package=\"PKG\") == \"\")")) - (invoke "autoreconf" "-vif"))) (add-before 'configure 'set-additional-environment-variables (lambda _ ;; Needed because of loompy @@ -10752,8 +10740,6 @@ (define-public pigx-scrnaseq r-singlecellexperiment r-stringr r-yaml)) - (native-inputs - (list autoconf automake)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for single-cell RNA sequencing experiments") (description -- cgit v1.2.3 From 964cdd57fa037fec4917ac76725b0a65d47483bc Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Sun, 5 Jun 2022 20:28:33 -0700 Subject: gnu: discrover: Use reproducible timestamps. * gnu/packages/bioinformatics.scm (discrover)[arguments]: Add 'set-force-source-date phase. --- gnu/packages/bioinformatics.scm | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 931eea7022..c53a2920ac 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3145,6 +3145,11 @@ (define-public discrover `(#:tests? #f ; there are no tests #:phases (modify-phases %standard-phases + (add-before 'build 'set-force-source-date + ;; for reproducible dates, texlive needs this to respect respect + ;; SOURCE_DATE_EPOCH + (lambda _ + (setenv "FORCE_SOURCE_DATE" "1"))) (add-after 'unpack 'fix-latex-errors (lambda _ (with-fluids ((%default-port-encoding #f)) -- cgit v1.2.3