aboutsummaryrefslogtreecommitdiff
path: root/gnu/packages
diff options
context:
space:
mode:
authorRicardo Wurmus <rekado@elephly.net>2022-04-05 17:26:00 +0200
committerRicardo Wurmus <rekado@elephly.net>2022-04-05 18:40:48 +0200
commit5d1c9fcdcf81bb95516f2d44e293c760300c9589 (patch)
tree860bb711478e61e4b329b7cc70b0b0f379267cdf /gnu/packages
parent029cb8c95f40f1b751b34d5e06c39c1db3a61ee1 (diff)
downloadguix-5d1c9fcdcf81bb95516f2d44e293c760300c9589.tar
guix-5d1c9fcdcf81bb95516f2d44e293c760300c9589.tar.gz
gnu: pigx-scrnaseq: Update to 1.1.8.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.8. [patches]: Remove. [native-inputs]: Remove. * gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioinformatics.scm12
-rw-r--r--gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch33
2 files changed, 3 insertions, 42 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index eed7e54f7f..3ad8800fdb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11132,7 +11132,7 @@ methylation and segmentation.")
(define-public pigx-scrnaseq
(package
(name "pigx-scrnaseq")
- (version "1.1.7")
+ (version "1.1.8")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
@@ -11140,20 +11140,14 @@ methylation and segmentation.")
"/pigx_scrnaseq-" version ".tar.gz"))
(sha256
(base32
- "1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx"))
- (patches (search-patches "pigx-scrnaseq-no-citeproc.patch"))))
+ "1lc42hl8mz95kilh0z39s3wnv092mhm6vl2i394n0yfvdzk4f885"))))
(build-system gnu-build-system)
(arguments
- `(#:phases
+ '(#:phases
(modify-phases %standard-phases
- (add-before 'bootstrap 'autoreconf
- (lambda _
- (invoke "autoreconf" "-vif")))
(add-before 'configure 'set-PYTHONPATH
(lambda _
(setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))))))
- (native-inputs
- (list automake 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
deleted file mode 100644
index 4cce33fb01..0000000000
--- a/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-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']