fb1ffc53ba
* 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.
34 lines
1.8 KiB
Diff
34 lines
1.8 KiB
Diff
diff -Naur pigx_bsseq-0.1.5/configure.ac pigx_bsseq-0.1.5.patched/configure.ac
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--- pigx_bsseq-0.1.5/configure.ac 2021-06-08 15:28:08.000000000 +0200
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+++ pigx_bsseq-0.1.5.patched/configure.ac 2021-10-05 14:43:56.806529137 +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([FASTQC], [fastqc])
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find_or_override_prog([MULTIQC], [multiqc])
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find_or_override_prog([TRIMGALORE], [trim_galore])
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diff -Naur pigx_bsseq-0.1.5/Makefile.in pigx_bsseq-0.1.5.patched/Makefile.in
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--- pigx_bsseq-0.1.5/Makefile.in 2021-06-08 16:17:03.000000000 +0200
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+++ pigx_bsseq-0.1.5.patched/Makefile.in 2021-10-05 14:43:34.635876855 +0200
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@@ -408,7 +408,6 @@
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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_bsseq-0.1.5/pigx-common/common/pigx-runner.in pigx_bsseq-0.1.5.patched/pigx-common/common/pigx-runner.in
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--- pigx_bsseq-0.1.5/pigx-common/common/pigx-runner.in 2021-06-08 10:14:29.000000000 +0200
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+++ pigx_bsseq-0.1.5.patched/pigx-common/common/pigx-runner.in 2021-10-05 14:43:44.296161069 +0200
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@@ -375,7 +375,6 @@
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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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