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authorLars-Dominik Braun <lars@6xq.net>2021-10-06 14:11:15 +0200
committerLars-Dominik Braun <lars@6xq.net>2021-10-08 09:13:55 +0200
commitc8a7ba621b99ee8e2e7cb0eb11637c446b5ec244 (patch)
tree5aa80e280ce756f9672d8852b1172531590d301e /gnu
parent26488f63b8e4845cc9ed6e91b0643936b5eaa509 (diff)
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.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/local.mk1
-rw-r--r--gnu/packages/bioinformatics.scm12
-rw-r--r--gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch33
3 files changed, 45 insertions, 1 deletions
diff --git a/gnu/local.mk b/gnu/local.mk
index 110980bef0..e74946a837 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1603,6 +1603,7 @@ dist_patch_DATA = \
%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 \
%D%/packages/patches/pingus-boost-headers.patch \
%D%/packages/patches/pingus-sdl-libs-config.patch \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f5de16877e..082e47bf5b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10732,8 +10732,18 @@ methylation and segmentation.")
"/pigx_scrnaseq-" version ".tar.gz"))
(sha256
(base32
- "1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx"))))
+ "1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx"))
+ (patches (search-patches "pigx-scrnaseq-no-citeproc.patch"))))
(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
`(("coreutils" ,coreutils)
("perl" ,perl)
diff --git a/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch b/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch
new file mode 100644
index 0000000000..4cce33fb01
--- /dev/null
+++ b/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch
@@ -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']