26488f63b8
* 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.
34 lines
1.8 KiB
Diff
34 lines
1.8 KiB
Diff
diff -Naur pigx_rnaseq-0.0.19/configure.ac pigx_rnaseq-0.0.19.patched/configure.ac
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--- pigx_rnaseq-0.0.19/configure.ac 2021-07-23 14:01:00.304391428 +0200
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+++ pigx_rnaseq-0.0.19.patched/configure.ac 2021-10-06 13:51:29.512960106 +0200
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@@ -38,7 +38,6 @@
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find_or_override_prog([GNUBASH], [bash])
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find_or_override_prog([SNAKEMAKE], [snakemake])
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find_or_override_prog([PANDOC], [pandoc])
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-find_or_override_prog([PANDOC_CITEPROC], [pandoc-citeproc])
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find_or_override_prog([STAR], [STAR])
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find_or_override_prog([HISAT2], [hisat2])
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find_or_override_prog([HISAT2_BUILD], [hisat2-build])
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diff -Naur pigx_rnaseq-0.0.19/Makefile.in pigx_rnaseq-0.0.19.patched/Makefile.in
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--- pigx_rnaseq-0.0.19/Makefile.in 2021-08-13 13:40:10.402922844 +0200
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+++ pigx_rnaseq-0.0.19.patched/Makefile.in 2021-10-06 13:51:04.052247524 +0200
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@@ -410,7 +410,6 @@
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PACKAGE_URL = @PACKAGE_URL@
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PACKAGE_VERSION = @PACKAGE_VERSION@
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PANDOC = @PANDOC@
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-PANDOC_CITEPROC = @PANDOC_CITEPROC@
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PATH_SEPARATOR = @PATH_SEPARATOR@
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PYTHON = @PYTHON@
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PYTHONPATH = @PYTHONPATH@
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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
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--- pigx_rnaseq-0.0.19/pigx-common/common/pigx-runner.in 2021-08-13 13:27:50.494352532 +0200
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+++ pigx_rnaseq-0.0.19.patched/pigx-common/common/pigx-runner.in 2021-10-06 13:51:38.798220108 +0200
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@@ -379,7 +379,6 @@
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if path.exists(bin): shutil.rmtree(bin)
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os.makedirs(bin, exist_ok=True)
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os.symlink('@PANDOC@', path.join(bin, "pandoc"))
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- os.symlink('@PANDOC_CITEPROC@', path.join(bin, "pandoc-citeproc"))
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os.symlink('@RSCRIPT@', path.join(bin, "Rscript"))
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os.environ['PATH'] = path.abspath(bin) + ":" + os.environ['PATH']
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os.environ['PIGX_PATH'] = path.abspath(bin) + ":" + os.environ['PATH']
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