gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc.
* 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.master
parent
26488f63b8
commit
c8a7ba621b
|
@ -1603,6 +1603,7 @@ dist_patch_DATA = \
|
||||||
%D%/packages/patches/pigx-chipseq-no-citeproc.patch \
|
%D%/packages/patches/pigx-chipseq-no-citeproc.patch \
|
||||||
%D%/packages/patches/pigx-rnaseq-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-sars-cov2-ww-no-citeproc.patch \
|
||||||
|
%D%/packages/patches/pigx-scrnaseq-no-citeproc.patch \
|
||||||
%D%/packages/patches/pinball-system-ltdl.patch \
|
%D%/packages/patches/pinball-system-ltdl.patch \
|
||||||
%D%/packages/patches/pingus-boost-headers.patch \
|
%D%/packages/patches/pingus-boost-headers.patch \
|
||||||
%D%/packages/patches/pingus-sdl-libs-config.patch \
|
%D%/packages/patches/pingus-sdl-libs-config.patch \
|
||||||
|
|
|
@ -10732,8 +10732,18 @@ methylation and segmentation.")
|
||||||
"/pigx_scrnaseq-" version ".tar.gz"))
|
"/pigx_scrnaseq-" version ".tar.gz"))
|
||||||
(sha256
|
(sha256
|
||||||
(base32
|
(base32
|
||||||
"1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx"))))
|
"1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx"))
|
||||||
|
(patches (search-patches "pigx-scrnaseq-no-citeproc.patch"))))
|
||||||
(build-system gnu-build-system)
|
(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
|
(inputs
|
||||||
`(("coreutils" ,coreutils)
|
`(("coreutils" ,coreutils)
|
||||||
("perl" ,perl)
|
("perl" ,perl)
|
||||||
|
|
|
@ -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']
|
Reference in New Issue