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| author | Lars-Dominik Braun <lars@6xq.net> | 2021-10-06 14:10:18 +0200 |
|---|---|---|
| committer | Lars-Dominik Braun <lars@6xq.net> | 2021-10-08 09:13:55 +0200 |
| commit | 26488f63b8e4845cc9ed6e91b0643936b5eaa509 (patch) | |
| tree | cb1c599f2daf2c64914c700a408dc0756335d6de /gnu/packages/patches | |
| parent | 07f2e4993b5b80008273de0bb756659321e74183 (diff) | |
gnu: pigx-rnaseq: Remove dependency on pandoc-citeproc.
* gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
Diffstat (limited to 'gnu/packages/patches')
| -rw-r--r-- | gnu/packages/patches/pigx-rnaseq-no-citeproc.patch | 33 |
1 files changed, 33 insertions, 0 deletions
diff --git a/gnu/packages/patches/pigx-rnaseq-no-citeproc.patch b/gnu/packages/patches/pigx-rnaseq-no-citeproc.patch new file mode 100644 index 0000000000..366ae3890a --- /dev/null +++ b/gnu/packages/patches/pigx-rnaseq-no-citeproc.patch @@ -0,0 +1,33 @@ +diff -Naur pigx_rnaseq-0.0.19/configure.ac pigx_rnaseq-0.0.19.patched/configure.ac +--- pigx_rnaseq-0.0.19/configure.ac 2021-07-23 14:01:00.304391428 +0200 ++++ pigx_rnaseq-0.0.19.patched/configure.ac 2021-10-06 13:51:29.512960106 +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([STAR], [STAR]) + find_or_override_prog([HISAT2], [hisat2]) + find_or_override_prog([HISAT2_BUILD], [hisat2-build]) +diff -Naur pigx_rnaseq-0.0.19/Makefile.in pigx_rnaseq-0.0.19.patched/Makefile.in +--- pigx_rnaseq-0.0.19/Makefile.in 2021-08-13 13:40:10.402922844 +0200 ++++ pigx_rnaseq-0.0.19.patched/Makefile.in 2021-10-06 13:51:04.052247524 +0200 +@@ -410,7 +410,6 @@ + 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_rnaseq-0.0.19/pigx-common/common/pigx-runner.in pigx_rnaseq-0.0.19.patched/pigx-common/common/pigx-runner.in +--- pigx_rnaseq-0.0.19/pigx-common/common/pigx-runner.in 2021-08-13 13:27:50.494352532 +0200 ++++ pigx_rnaseq-0.0.19.patched/pigx-common/common/pigx-runner.in 2021-10-06 13:51:38.798220108 +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'] |