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

* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-chipseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
master
Lars-Dominik Braun 2021-10-06 14:08:53 +02:00
parent e51a3f4a72
commit 07f2e4993b
No known key found for this signature in database
GPG Key ID: F663943E08D8092A
3 changed files with 46 additions and 4 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-chipseq-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 \

16
gnu/packages/bioinformatics.scm
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@ -10567,10 +10567,16 @@ expression report comparing samples in an easily configurable manner.")
"/pigx_chipseq-" version ".tar.gz"))
(sha256
(base32
"0c6npx35sszycf059w1x1k4k9hq1qqxny0i4p57q1188czr4561h"))))
"0c6npx35sszycf059w1x1k4k9hq1qqxny0i4p57q1188czr4561h"))
(patches (search-patches "pigx-chipseq-no-citeproc.patch"))))
(build-system gnu-build-system)
;; parts of the tests rely on access to the network
(arguments '(#:tests? #f))
(arguments
`(#:tests? #f ; parts of the tests rely on access to the network
#:phases
(modify-phases %standard-phases
(add-before 'bootstrap 'autoreconf
(lambda _
(invoke "autoreconf" "-vif"))))))
(inputs
`(("grep" ,grep)
("coreutils" ,coreutils)
@ -10621,7 +10627,9 @@ expression report comparing samples in an easily configurable manner.")
("bedtools" ,bedtools)
("kentutils" ,kentutils)))
(native-inputs
`(("python-pytest" ,python-pytest)))
`(("autoconf" ,autoconf)
("automake" ,automake)
("python-pytest" ,python-pytest)))
(home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipeline for ChIP sequencing experiments")
(description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak

33
gnu/packages/patches/pigx-chipseq-no-citeproc.patch 100644
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@ -0,0 +1,33 @@
diff -Naur pigx_chipseq-0.0.53/configure.ac pigx_chipseq-0.0.53.patched/configure.ac
--- pigx_chipseq-0.0.53/configure.ac 2021-09-28 11:14:12.000000000 +0200
+++ pigx_chipseq-0.0.53.patched/configure.ac 2021-10-07 14:48:53.034054327 +0200
@@ -52,7 +52,6 @@
find_or_override_prog([MACS2], [macs2])
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([BOWTIE2], [bowtie2])
find_or_override_prog([BOWTIE2_BUILD], [bowtie2-build])
diff -Naur pigx_chipseq-0.0.53/Makefile.in pigx_chipseq-0.0.53.patched/Makefile.in
--- pigx_chipseq-0.0.53/Makefile.in 2021-09-28 11:55:05.000000000 +0200
+++ pigx_chipseq-0.0.53.patched/Makefile.in 2021-10-07 14:48:37.195577143 +0200
@@ -407,7 +407,6 @@
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_chipseq-0.0.53/pigx-common/common/pigx-runner.in pigx_chipseq-0.0.53.patched/pigx-common/common/pigx-runner.in
--- pigx_chipseq-0.0.53/pigx-common/common/pigx-runner.in 2021-09-27 18:16:42.000000000 +0200
+++ pigx_chipseq-0.0.53.patched/pigx-common/common/pigx-runner.in 2021-10-07 14:48:44.200788218 +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']