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24/24: gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc.
From: |
guix-commits |
Subject: |
24/24: gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc. |
Date: |
Fri, 8 Oct 2021 03:20:59 -0400 (EDT) |
lbraun pushed a commit to branch master
in repository guix.
commit c8a7ba621b99ee8e2e7cb0eb11637c446b5ec244
Author: Lars-Dominik Braun <lars@6xq.net>
AuthorDate: Wed Oct 6 14:11:15 2021 +0200
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.
---
gnu/local.mk | 1 +
gnu/packages/bioinformatics.scm | 12 +++++++-
.../patches/pigx-scrnaseq-no-citeproc.patch | 33 ++++++++++++++++++++++
3 files changed, 45 insertions(+), 1 deletion(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index 110980b..e74946a 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 f5de168..082e47b 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 0000000..4cce33f
--- /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']
- 13/24: gnu: ruby-pandoc-ruby: Disable tests., (continued)
- 13/24: gnu: ruby-pandoc-ruby: Disable tests., guix-commits, 2021/10/08
- 14/24: gnu: ghc-silently: Remove unused input., guix-commits, 2021/10/08
- 16/24: gnu: ngless: Fix build., guix-commits, 2021/10/08
- 17/24: gnu: python-pypandoc: Upgrade to 1.6.4., guix-commits, 2021/10/08
- 18/24: gnu: ghc-repline: Remove version 0.2.0.0., guix-commits, 2021/10/08
- 19/24: gnu: ghc-haskeline: Remove version postfix from variable name., guix-commits, 2021/10/08
- 22/24: gnu: pigx-chipseq: Remove dependency on pandoc-citeproc., guix-commits, 2021/10/08
- 20/24: gnu: pigx-bsseq: Remove dependency on pandoc-citeproc., guix-commits, 2021/10/08
- 21/24: gnu: pigx-sars-cov2-ww: Remove dependency on pandoc-citeproc., guix-commits, 2021/10/08
- 23/24: gnu: pigx-rnaseq: Remove dependency on pandoc-citeproc., guix-commits, 2021/10/08
- 24/24: gnu: pigx-scrnaseq: Remove dependency on pandoc-citeproc.,
guix-commits <=