c8a7ba621b
* gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[source]: Use it. [native-inputs]: Add automake/autoconf.
34 lines
1.7 KiB
Diff
34 lines
1.7 KiB
Diff
diff -Naur pigx_scrnaseq-1.1.7/configure.ac pigx_scrnaseq-1.1.7.patched/configure.ac
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--- pigx_scrnaseq-1.1.7/configure.ac 2020-03-17 14:37:46.000000000 +0100
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+++ pigx_scrnaseq-1.1.7.patched/configure.ac 2021-10-06 13:55:49.779271317 +0200
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@@ -43,7 +43,6 @@
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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([STAR], [STAR])
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find_or_override_prog([SAMTOOLS], [samtools])
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diff -Naur pigx_scrnaseq-1.1.7/Makefile.in pigx_scrnaseq-1.1.7.patched/Makefile.in
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--- pigx_scrnaseq-1.1.7/Makefile.in 2020-11-30 16:55:48.000000000 +0100
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+++ pigx_scrnaseq-1.1.7.patched/Makefile.in 2021-10-06 13:55:52.224340194 +0200
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@@ -395,7 +395,6 @@
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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_scrnaseq-1.1.7/pigx-scrnaseq.in pigx_scrnaseq-1.1.7.patched/pigx-scrnaseq.in
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--- pigx_scrnaseq-1.1.7/pigx-scrnaseq.in 2020-11-30 16:08:55.000000000 +0100
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+++ pigx_scrnaseq-1.1.7.patched/pigx-scrnaseq.in 2021-10-06 13:55:47.889218079 +0200
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@@ -274,7 +274,6 @@
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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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