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

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* gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
This commit is contained in:
Lars-Dominik Braun 2021-10-06 14:10:18 +02:00
parent 07f2e4993b
commit 26488f63b8
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GPG key ID: F663943E08D8092A
3 changed files with 42 additions and 2 deletions
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1
gnu/local.mk
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@ -1601,6 +1601,7 @@ dist_patch_DATA = \
%D%/packages/patches/pidgin-add-search-path.patch \
%D%/packages/patches/pigx-bsseq-no-citeproc.patch \
%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/pinball-system-ltdl.patch \
%D%/packages/patches/pingus-boost-headers.patch \

10
gnu/packages/bioinformatics.scm
View file

@ -10489,7 +10489,8 @@ once. This package provides tools to perform Drop-seq analyses.")
"/pigx_rnaseq-" version ".tar.gz"))
(sha256
(base32
"1ja3bda1appxrzbfy7wp7khy30mm7lic8xbq3gkbpc5bld3as9cm"))))
"1ja3bda1appxrzbfy7wp7khy30mm7lic8xbq3gkbpc5bld3as9cm"))
(patches (search-patches "pigx-rnaseq-no-citeproc.patch"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-tests? #f ; not supported
@ -10502,6 +10503,9 @@ once. This package provides tools to perform Drop-seq analyses.")
(substitute* "Makefile.in"
(("^ tests/test_multiqc/test.sh") "")
(("^ test.sh") ""))))
(add-before 'bootstrap 'autoreconf
(lambda _
(invoke "autoreconf" "-vif")))
(add-before 'check 'set-timezone
;; The readr package is picky about timezones.
(lambda* (#:key inputs #:allow-other-keys)
@ -10545,7 +10549,9 @@ once. This package provides tools to perform Drop-seq analyses.")
("python-deeptools" ,python-deeptools)
("python-pyyaml" ,python-pyyaml)))
(native-inputs
`(("tzdata" ,tzdata)))
`(("tzdata" ,tzdata)
("automake" ,automake)
("autoconf" ,autoconf)))
(home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipeline for RNA sequencing experiments")
(description "PiGX RNAseq is an analysis pipeline for preprocessing and

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

@ -0,0 +1,33 @@
diff -Naur pigx_rnaseq-0.0.19/configure.ac pigx_rnaseq-0.0.19.patched/configure.ac
--- pigx_rnaseq-0.0.19/configure.ac 2021-07-23 14:01:00.304391428 +0200
+++ pigx_rnaseq-0.0.19.patched/configure.ac 2021-10-06 13:51:29.512960106 +0200
@@ -38,7 +38,6 @@
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([STAR], [STAR])
find_or_override_prog([HISAT2], [hisat2])
find_or_override_prog([HISAT2_BUILD], [hisat2-build])
diff -Naur pigx_rnaseq-0.0.19/Makefile.in pigx_rnaseq-0.0.19.patched/Makefile.in
--- pigx_rnaseq-0.0.19/Makefile.in 2021-08-13 13:40:10.402922844 +0200
+++ pigx_rnaseq-0.0.19.patched/Makefile.in 2021-10-06 13:51:04.052247524 +0200
@@ -410,7 +410,6 @@
PACKAGE_URL = @PACKAGE_URL@
PACKAGE_VERSION = @PACKAGE_VERSION@
PANDOC = @PANDOC@
-PANDOC_CITEPROC = @PANDOC_CITEPROC@
PATH_SEPARATOR = @PATH_SEPARATOR@
PYTHON = @PYTHON@
PYTHONPATH = @PYTHONPATH@
diff -Naur pigx_rnaseq-0.0.19/pigx-common/common/pigx-runner.in pigx_rnaseq-0.0.19.patched/pigx-common/common/pigx-runner.in
--- pigx_rnaseq-0.0.19/pigx-common/common/pigx-runner.in 2021-08-13 13:27:50.494352532 +0200
+++ pigx_rnaseq-0.0.19.patched/pigx-common/common/pigx-runner.in 2021-10-06 13:51:38.798220108 +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']