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22/24: gnu: pigx-chipseq: Remove dependency on pandoc-citeproc.
From: |
guix-commits |
Subject: |
22/24: gnu: pigx-chipseq: Remove dependency on pandoc-citeproc. |
Date: |
Fri, 8 Oct 2021 03:20:57 -0400 (EDT) |
lbraun pushed a commit to branch master
in repository guix.
commit 07f2e4993b5b80008273de0bb756659321e74183
Author: Lars-Dominik Braun <lars@6xq.net>
AuthorDate: Wed Oct 6 14:08:53 2021 +0200
gnu: pigx-chipseq: Remove dependency on pandoc-citeproc.
* gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Add patch.
* gnu/local.mk: Register it.
* gnu/packages/bioinformatics.scm (pigx-chipseq)[source]: Use it.
[native-inputs]: Add automake/autoconf.
---
gnu/local.mk | 1 +
gnu/packages/bioinformatics.scm | 16 ++++++++---
.../patches/pigx-chipseq-no-citeproc.patch | 33 ++++++++++++++++++++++
3 files changed, 46 insertions(+), 4 deletions(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index 9c8a777..71f1a25 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1600,6 +1600,7 @@ 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/pigx-sars-cov2-ww-no-citeproc.patch \
%D%/packages/patches/pinball-system-ltdl.patch \
%D%/packages/patches/pingus-boost-headers.patch \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ed4470e..150bbc3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10567,10 +10567,16 @@ expression report comparing samples in an easily
configurable manner.")
"/pigx_chipseq-" version ".tar.gz"))
(sha256
(base32
- "0c6npx35sszycf059w1x1k4k9hq1qqxny0i4p57q1188czr4561h"))))
+ "0c6npx35sszycf059w1x1k4k9hq1qqxny0i4p57q1188czr4561h"))
+ (patches (search-patches "pigx-chipseq-no-citeproc.patch"))))
(build-system gnu-build-system)
- ;; parts of the tests rely on access to the network
- (arguments '(#:tests? #f))
+ (arguments
+ `(#:tests? #f ; parts of the tests rely on access to the network
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'bootstrap 'autoreconf
+ (lambda _
+ (invoke "autoreconf" "-vif"))))))
(inputs
`(("grep" ,grep)
("coreutils" ,coreutils)
@@ -10621,7 +10627,9 @@ expression report comparing samples in an easily
configurable manner.")
("bedtools" ,bedtools)
("kentutils" ,kentutils)))
(native-inputs
- `(("python-pytest" ,python-pytest)))
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("python-pytest" ,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
diff --git a/gnu/packages/patches/pigx-chipseq-no-citeproc.patch
b/gnu/packages/patches/pigx-chipseq-no-citeproc.patch
new file mode 100644
index 0000000..b01820f
--- /dev/null
+++ b/gnu/packages/patches/pigx-chipseq-no-citeproc.patch
@@ -0,0 +1,33 @@
+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']
- 10/24: gnu: Update Haskell ecosystem., (continued)
- 10/24: gnu: Update Haskell ecosystem., guix-commits, 2021/10/08
- 11/24: gnu: cabal-install: Build with GHC 8.10., guix-commits, 2021/10/08
- 12/24: gnu: hedgewars: Fix build., guix-commits, 2021/10/08
- 15/24: gnu: idris: Fix build., guix-commits, 2021/10/08
- 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 <=
- 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, 2021/10/08