diff options
| author | Lars-Dominik Braun <lars@6xq.net> | 2021-10-06 14:11:15 +0200 |
|---|---|---|
| committer | Lars-Dominik Braun <lars@6xq.net> | 2021-10-08 09:13:55 +0200 |
| commit | c8a7ba621b99ee8e2e7cb0eb11637c446b5ec244 (patch) | |
| tree | 5aa80e280ce756f9672d8852b1172531590d301e /gnu | |
| parent | 26488f63b8e4845cc9ed6e91b0643936b5eaa509 (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.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 12 | ||||
| -rw-r--r-- | gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch | 33 |
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'] |