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| author | Lars-Dominik Braun <lars@6xq.net> | 2021-10-05 15:42:38 +0200 |
|---|---|---|
| committer | Lars-Dominik Braun <lars@6xq.net> | 2021-10-08 09:13:54 +0200 |
| commit | fb1ffc53ba6177e28aa296ae2e9c2e812f92e28e (patch) | |
| tree | 86674f7b7fb0b8fa628d73c648b535ab174ca94c /gnu/packages/patches | |
| parent | ff5fea3dfe64b933f7698134de9dba14ef8d0694 (diff) | |
gnu: pigx-bsseq: Remove dependency on pandoc-citeproc.
* gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-bsseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
Diffstat (limited to 'gnu/packages/patches')
| -rw-r--r-- | gnu/packages/patches/pigx-bsseq-no-citeproc.patch | 33 |
1 files changed, 33 insertions, 0 deletions
diff --git a/gnu/packages/patches/pigx-bsseq-no-citeproc.patch b/gnu/packages/patches/pigx-bsseq-no-citeproc.patch new file mode 100644 index 0000000000..882e660fe4 --- /dev/null +++ b/gnu/packages/patches/pigx-bsseq-no-citeproc.patch @@ -0,0 +1,33 @@ +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'] |