diff options
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 19 | ||||
| -rw-r--r-- | gnu/packages/patches/pigx-chipseq-no-citeproc.patch | 33 |
3 files changed, 3 insertions, 50 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index af92253ddd..b9d62a3f0f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1629,7 +1629,6 @@ dist_patch_DATA = \ %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/pigx-chipseq-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 1ffac1a0ca..f2800d3163 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10526,7 +10526,7 @@ expression report comparing samples in an easily configurable manner.") (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 @@ expression report comparing samples in an easily configurable manner.") "/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 @@ expression report comparing samples in an easily configurable manner.") 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 diff --git a/gnu/packages/patches/pigx-chipseq-no-citeproc.patch b/gnu/packages/patches/pigx-chipseq-no-citeproc.patch deleted file mode 100644 index b01820f110..0000000000 --- a/gnu/packages/patches/pigx-chipseq-no-citeproc.patch +++ /dev/null @@ -1,33 +0,0 @@ -diff -Naur pigx_chipseq-0.0.53/configure.ac pigx_chipseq-0.0.53.patched/configure.ac ---- pigx_chipseq-0.0.53/configure.ac 2021-09-28 11:14:12.000000000 +0200 -+++ pigx_chipseq-0.0.53.patched/configure.ac 2021-10-07 14:48:53.034054327 +0200 -@@ -52,7 +52,6 @@ - find_or_override_prog([MACS2], [macs2]) - 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([BOWTIE2], [bowtie2]) - find_or_override_prog([BOWTIE2_BUILD], [bowtie2-build]) -diff -Naur pigx_chipseq-0.0.53/Makefile.in pigx_chipseq-0.0.53.patched/Makefile.in ---- pigx_chipseq-0.0.53/Makefile.in 2021-09-28 11:55:05.000000000 +0200 -+++ pigx_chipseq-0.0.53.patched/Makefile.in 2021-10-07 14:48:37.195577143 +0200 -@@ -407,7 +407,6 @@ - PACKAGE_URL = @PACKAGE_URL@ - PACKAGE_VERSION = @PACKAGE_VERSION@ - PANDOC = @PANDOC@ --PANDOC_CITEPROC = @PANDOC_CITEPROC@ - PATH_SEPARATOR = @PATH_SEPARATOR@ - PERL = @PERL@ - PYTHON = @PYTHON@ -diff -Naur pigx_chipseq-0.0.53/pigx-common/common/pigx-runner.in pigx_chipseq-0.0.53.patched/pigx-common/common/pigx-runner.in ---- pigx_chipseq-0.0.53/pigx-common/common/pigx-runner.in 2021-09-27 18:16:42.000000000 +0200 -+++ pigx_chipseq-0.0.53.patched/pigx-common/common/pigx-runner.in 2021-10-07 14:48:44.200788218 +0200 -@@ -379,7 +379,6 @@ - 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'] |