e51a3f4a72
* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Add patch. * gnu/local.mk: Register it. * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[source]: Use it. [native-inputs]: Add automake/autoconf.
34 lines
1.8 KiB
Diff
34 lines
1.8 KiB
Diff
diff -Naur pigx_sars-cov2-ww-0.0.3/configure.ac pigx_sars-cov2-ww-0.0.3.patched/configure.ac
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--- pigx_sars-cov2-ww-0.0.3/configure.ac 2021-06-10 10:12:00.552889984 +0200
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+++ pigx_sars-cov2-ww-0.0.3.patched/configure.ac 2021-10-05 14:52:32.318695129 +0200
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@@ -50,7 +50,6 @@
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find_or_override_prog([MULTIQC], [multiqc])
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find_or_override_prog([WGET], [wget])
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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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AC_ARG_ENABLE([r-packages-check],
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AS_HELP_STRING([--disable-r-packages-check], [Do not check any R packages.]),
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diff -Naur pigx_sars-cov2-ww-0.0.3/Makefile.in pigx_sars-cov2-ww-0.0.3.patched/Makefile.in
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--- pigx_sars-cov2-ww-0.0.3/Makefile.in 2021-08-05 16:33:59.164123383 +0200
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+++ pigx_sars-cov2-ww-0.0.3.patched/Makefile.in 2021-10-05 14:52:41.272958547 +0200
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@@ -402,7 +402,6 @@
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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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PRINSEQ = @PRINSEQ@
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PYTHON = @PYTHON@
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diff -Naur pigx_sars-cov2-ww-0.0.3/pigx-common/common/pigx-runner.in pigx_sars-cov2-ww-0.0.3.patched/pigx-common/common/pigx-runner.in
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--- pigx_sars-cov2-ww-0.0.3/pigx-common/common/pigx-runner.in 2021-07-30 11:10:17.913115902 +0200
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+++ pigx_sars-cov2-ww-0.0.3.patched/pigx-common/common/pigx-runner.in 2021-10-05 14:52:23.602438714 +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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