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gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc.

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* 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.
This commit is contained in:
Lars-Dominik Braun 2021-10-05 19:08:36 +02:00
parent fb1ffc53ba
commit e51a3f4a72
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GPG key ID: F663943E08D8092A
3 changed files with 45 additions and 1 deletions
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1
gnu/local.mk
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@ -1600,6 +1600,7 @@ dist_patch_DATA = \
%D%/packages/patches/picprog-non-intel-support.patch \
%D%/packages/patches/pidgin-add-search-path.patch \
%D%/packages/patches/pigx-bsseq-no-citeproc.patch \
%D%/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch \
%D%/packages/patches/pinball-system-ltdl.patch \
%D%/packages/patches/pingus-boost-headers.patch \
%D%/packages/patches/pingus-sdl-libs-config.patch \

12
gnu/packages/bioinformatics.scm
View file

@ -10783,8 +10783,18 @@ (define-public pigx-sars-cov2-ww
"/pigx_sars-cov2-ww-" version ".tar.gz"))
(sha256
(base32
"1hhdbwsnl0d37lrmisw5hr630xr8s41qvxflm05anh11rj8n22yw"))))
"1hhdbwsnl0d37lrmisw5hr630xr8s41qvxflm05anh11rj8n22yw"))
(patches (search-patches "pigx-sars-cov2-ww-no-citeproc.patch"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-before 'bootstrap 'autoreconf
(lambda _
(invoke "autoreconf" "-vif"))))))
(native-inputs
`(("automake" ,automake)
("autoconf" ,autoconf)))
(inputs
`(("bash-minimal" ,bash-minimal)
("bwa" ,bwa)

33
gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch Normal file
View file

@ -0,0 +1,33 @@
diff -Naur pigx_sars-cov2-ww-0.0.3/configure.ac pigx_sars-cov2-ww-0.0.3.patched/configure.ac
--- pigx_sars-cov2-ww-0.0.3/configure.ac 2021-06-10 10:12:00.552889984 +0200
+++ pigx_sars-cov2-ww-0.0.3.patched/configure.ac 2021-10-05 14:52:32.318695129 +0200
@@ -50,7 +50,6 @@
find_or_override_prog([MULTIQC], [multiqc])
find_or_override_prog([WGET], [wget])
find_or_override_prog([PANDOC], [pandoc])
-find_or_override_prog([PANDOC_CITEPROC], [pandoc-citeproc])
AC_ARG_ENABLE([r-packages-check],
AS_HELP_STRING([--disable-r-packages-check], [Do not check any R packages.]),
diff -Naur pigx_sars-cov2-ww-0.0.3/Makefile.in pigx_sars-cov2-ww-0.0.3.patched/Makefile.in
--- pigx_sars-cov2-ww-0.0.3/Makefile.in 2021-08-05 16:33:59.164123383 +0200
+++ pigx_sars-cov2-ww-0.0.3.patched/Makefile.in 2021-10-05 14:52:41.272958547 +0200
@@ -402,7 +402,6 @@
PACKAGE_URL = @PACKAGE_URL@
PACKAGE_VERSION = @PACKAGE_VERSION@
PANDOC = @PANDOC@
-PANDOC_CITEPROC = @PANDOC_CITEPROC@
PATH_SEPARATOR = @PATH_SEPARATOR@
PRINSEQ = @PRINSEQ@
PYTHON = @PYTHON@
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
--- pigx_sars-cov2-ww-0.0.3/pigx-common/common/pigx-runner.in 2021-07-30 11:10:17.913115902 +0200
+++ pigx_sars-cov2-ww-0.0.3.patched/pigx-common/common/pigx-runner.in 2021-10-05 14:52:23.602438714 +0200
@@ -379,7 +379,6 @@
if path.exists(bin): shutil.rmtree(bin)
os.makedirs(bin, exist_ok=True)
os.symlink('@PANDOC@', path.join(bin, "pandoc"))
- os.symlink('@PANDOC_CITEPROC@', path.join(bin, "pandoc-citeproc"))
os.symlink('@RSCRIPT@', path.join(bin, "Rscript"))
os.environ['PATH'] = path.abspath(bin) + ":" + os.environ['PATH']
os.environ['PIGX_PATH'] = path.abspath(bin) + ":" + os.environ['PATH']