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gnu: pigx-rnaseq: Update to 0.0.20.

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* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.20.
[source]: Remove patch.
[inputs]: Add megadepth.
* gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
This commit is contained in:
Ricardo Wurmus 2022-03-29 13:42:48 +02:00
parent 3b0c9e4c20
commit 847acc3206
No known key found for this signature in database
GPG key ID: 197A5888235FACAC
3 changed files with 3 additions and 37 deletions
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1
gnu/local.mk
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@ -1628,7 +1628,6 @@ 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/pigx-scrnaseq-no-citeproc.patch \
%D%/packages/patches/pinball-system-ltdl.patch \

6
gnu/packages/bioinformatics.scm
View file

@ -10869,7 +10869,7 @@ (define-public dropseq-tools
(define-public pigx-rnaseq
(package
(name "pigx-rnaseq")
(version "0.0.19")
(version "0.0.20")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
@ -10877,8 +10877,7 @@ (define-public pigx-rnaseq
"/pigx_rnaseq-" version ".tar.gz"))
(sha256
(base32
"1ja3bda1appxrzbfy7wp7khy30mm7lic8xbq3gkbpc5bld3as9cm"))
(patches (search-patches "pigx-rnaseq-no-citeproc.patch"))))
"0bf65qqvlkc77vl7cmmzacq70f0qav4p6nf8pp3x1vdd0nvhr24f"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-tests? #f ; not supported
@ -10909,6 +10908,7 @@ (define-public pigx-rnaseq
sed
gzip
snakemake
megadepth
multiqc
star-for-pigx
hisat2

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

@ -1,33 +0,0 @@
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']