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gnu: pigx-chipseq: Update to 0.1.0.

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* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.1.0.
[source]: Remove patch.
[arguments]: Remove 'autoreconf phase.
[native-inputs]: Remove autoconf and automake.
* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
This commit is contained in:
Ricardo Wurmus 2022-06-01 12:18:00 +02:00
parent 75af73e1b7
commit 6e54ce9ca9
No known key found for this signature in database
GPG key ID: 197A5888235FACAC
3 changed files with 3 additions and 50 deletions
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1
gnu/local.mk
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@ -1629,7 +1629,6 @@ 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/pinball-system-ltdl.patch \
%D%/packages/patches/pingus-boost-headers.patch \
%D%/packages/patches/pingus-sdl-libs-config.patch \

19
gnu/packages/bioinformatics.scm
View file

@ -10526,7 +10526,7 @@ expression report comparing samples in an easily configurable manner.")
(define-public pigx-chipseq
(package
(name "pigx-chipseq")
(version "0.0.53")
(version "0.1.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
@ -10534,25 +10534,12 @@ expression report comparing samples in an easily configurable manner.")
"/pigx_chipseq-" version ".tar.gz"))
(sha256
(base32
"0c6npx35sszycf059w1x1k4k9hq1qqxny0i4p57q1188czr4561h"))
(patches (search-patches "pigx-chipseq-no-citeproc.patch"))))
"008n6drj9q5av86xihxlj4py2c9p3c5z5ld89c3bksrp77zxiy67"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; parts of the tests rely on access to the network
#:phases
(modify-phases %standard-phases
(add-before 'bootstrap 'autoreconf
(lambda _
;; This was fixed in commit
;; 0b1c9f7f2e4d0ff601f1de95ab8b2953f4d5dbc7, but there is no
;; release with this fix.
(call-with-output-file "VERSION"
(lambda (port) (display ,version port)))
;; See https://github.com/BIMSBbioinfo/pigx_chipseq/issues/176
(substitute* "m4/ax_r_package.m4"
(("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)")
"if(system.file(package=\"PKG\") == \"\")"))
(invoke "autoreconf" "-vif")))
(add-before 'configure 'set-PYTHONPATH
(lambda _
(setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))))))
@ -10606,7 +10593,7 @@ expression report comparing samples in an easily configurable manner.")
bedtools
kentutils))
(native-inputs
(list autoconf automake python-pytest))
(list 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
View file

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