07f2e4993b
* 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.
34 lines
1.8 KiB
Diff
34 lines
1.8 KiB
Diff
diff -Naur pigx_chipseq-0.0.53/configure.ac pigx_chipseq-0.0.53.patched/configure.ac
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--- pigx_chipseq-0.0.53/configure.ac 2021-09-28 11:14:12.000000000 +0200
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+++ pigx_chipseq-0.0.53.patched/configure.ac 2021-10-07 14:48:53.034054327 +0200
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@@ -52,7 +52,6 @@
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find_or_override_prog([MACS2], [macs2])
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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([BOWTIE2], [bowtie2])
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find_or_override_prog([BOWTIE2_BUILD], [bowtie2-build])
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diff -Naur pigx_chipseq-0.0.53/Makefile.in pigx_chipseq-0.0.53.patched/Makefile.in
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--- pigx_chipseq-0.0.53/Makefile.in 2021-09-28 11:55:05.000000000 +0200
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+++ pigx_chipseq-0.0.53.patched/Makefile.in 2021-10-07 14:48:37.195577143 +0200
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@@ -407,7 +407,6 @@
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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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PERL = @PERL@
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PYTHON = @PYTHON@
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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
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--- pigx_chipseq-0.0.53/pigx-common/common/pigx-runner.in 2021-09-27 18:16:42.000000000 +0200
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+++ pigx_chipseq-0.0.53.patched/pigx-common/common/pigx-runner.in 2021-10-07 14:48:44.200788218 +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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