diff options
| author | Lars-Dominik Braun <lars@6xq.net> | 2021-10-06 14:08:53 +0200 |
|---|---|---|
| committer | Lars-Dominik Braun <lars@6xq.net> | 2021-10-08 09:13:54 +0200 |
| commit | 07f2e4993b5b80008273de0bb756659321e74183 (patch) | |
| tree | 8c8d779d41e09e5b4929bdbf2ee10ce4f32b9431 /gnu/packages/patches | |
| parent | e51a3f4a727d8bd74ccef6322a422c7e8a421394 (diff) | |
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.
Diffstat (limited to 'gnu/packages/patches')
| -rw-r--r-- | gnu/packages/patches/pigx-chipseq-no-citeproc.patch | 33 |
1 files changed, 33 insertions, 0 deletions
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'] |