From 07f2e4993b5b80008273de0bb756659321e74183 Mon Sep 17 00:00:00 2001 From: Lars-Dominik Braun Date: Wed, 6 Oct 2021 14:08:53 +0200 Subject: gnu: pigx-chipseq: Remove dependency on pandoc-citeproc. * gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-chipseq)[source]: Use it. [native-inputs]: Add automake/autoconf. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 16 ++++++++--- .../patches/pigx-chipseq-no-citeproc.patch | 33 ++++++++++++++++++++++ 3 files changed, 46 insertions(+), 4 deletions(-) create mode 100644 gnu/packages/patches/pigx-chipseq-no-citeproc.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 9c8a777d19..71f1a25f83 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1600,6 +1600,7 @@ 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/pigx-sars-cov2-ww-no-citeproc.patch \ %D%/packages/patches/pinball-system-ltdl.patch \ %D%/packages/patches/pingus-boost-headers.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ed4470e313..150bbc361f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10567,10 +10567,16 @@ expression report comparing samples in an easily configurable manner.") "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "0c6npx35sszycf059w1x1k4k9hq1qqxny0i4p57q1188czr4561h")))) + "0c6npx35sszycf059w1x1k4k9hq1qqxny0i4p57q1188czr4561h")) + (patches (search-patches "pigx-chipseq-no-citeproc.patch")))) (build-system gnu-build-system) - ;; parts of the tests rely on access to the network - (arguments '(#:tests? #f)) + (arguments + `(#:tests? #f ; parts of the tests rely on access to the network + #:phases + (modify-phases %standard-phases + (add-before 'bootstrap 'autoreconf + (lambda _ + (invoke "autoreconf" "-vif")))))) (inputs `(("grep" ,grep) ("coreutils" ,coreutils) @@ -10621,7 +10627,9 @@ expression report comparing samples in an easily configurable manner.") ("bedtools" ,bedtools) ("kentutils" ,kentutils))) (native-inputs - `(("python-pytest" ,python-pytest))) + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("python-pytest" ,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 new file mode 100644 index 0000000000..b01820f110 --- /dev/null +++ b/gnu/packages/patches/pigx-chipseq-no-citeproc.patch @@ -0,0 +1,33 @@ +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'] -- cgit v1.2.3