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gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc.

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* 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.
This commit is contained in:
Lars-Dominik Braun 2021-10-06 14:11:15 +02:00
parent 26488f63b8
commit c8a7ba621b
No known key found for this signature in database
GPG key ID: F663943E08D8092A
3 changed files with 45 additions and 1 deletions
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1
gnu/local.mk
View file

@ -1603,6 +1603,7 @@ dist_patch_DATA = \
%D%/packages/patches/pigx-chipseq-no-citeproc.patch \
%D%/packages/patches/pigx-rnaseq-no-citeproc.patch \
%D%/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch \
%D%/packages/patches/pigx-scrnaseq-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

@ -10732,8 +10732,18 @@ methylation and segmentation.")
"/pigx_scrnaseq-" version ".tar.gz"))
(sha256
(base32
"1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx"))))
"1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx"))
(patches (search-patches "pigx-scrnaseq-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
`(("coreutils" ,coreutils)
("perl" ,perl)

33
gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch Normal file
View file

@ -0,0 +1,33 @@
diff -Naur pigx_scrnaseq-1.1.7/configure.ac pigx_scrnaseq-1.1.7.patched/configure.ac
--- pigx_scrnaseq-1.1.7/configure.ac 2020-03-17 14:37:46.000000000 +0100
+++ pigx_scrnaseq-1.1.7.patched/configure.ac 2021-10-06 13:55:49.779271317 +0200
@@ -43,7 +43,6 @@
find_or_override_prog([GNUBASH], [bash])
find_or_override_prog([SNAKEMAKE], [snakemake])
find_or_override_prog([PANDOC], [pandoc])
-find_or_override_prog([PANDOC_CITEPROC], [pandoc-citeproc])
find_or_override_prog([FASTQC], [fastqc])
find_or_override_prog([STAR], [STAR])
find_or_override_prog([SAMTOOLS], [samtools])
diff -Naur pigx_scrnaseq-1.1.7/Makefile.in pigx_scrnaseq-1.1.7.patched/Makefile.in
--- pigx_scrnaseq-1.1.7/Makefile.in 2020-11-30 16:55:48.000000000 +0100
+++ pigx_scrnaseq-1.1.7.patched/Makefile.in 2021-10-06 13:55:52.224340194 +0200
@@ -395,7 +395,6 @@
PACKAGE_URL = @PACKAGE_URL@
PACKAGE_VERSION = @PACKAGE_VERSION@
PANDOC = @PANDOC@
-PANDOC_CITEPROC = @PANDOC_CITEPROC@
PATH_SEPARATOR = @PATH_SEPARATOR@
PERL = @PERL@
PYTHON = @PYTHON@
diff -Naur pigx_scrnaseq-1.1.7/pigx-scrnaseq.in pigx_scrnaseq-1.1.7.patched/pigx-scrnaseq.in
--- pigx_scrnaseq-1.1.7/pigx-scrnaseq.in 2020-11-30 16:08:55.000000000 +0100
+++ pigx_scrnaseq-1.1.7.patched/pigx-scrnaseq.in 2021-10-06 13:55:47.889218079 +0200
@@ -274,7 +274,6 @@
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']