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branch master updated: gnu: pigx-rnaseq: Update to 0.0.17.
From: |
guix-commits |
Subject: |
branch master updated: gnu: pigx-rnaseq: Update to 0.0.17. |
Date: |
Mon, 07 Jun 2021 18:53:34 -0400 |
This is an automated email from the git hooks/post-receive script.
rekado pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new 4a01e00 gnu: pigx-rnaseq: Update to 0.0.17.
4a01e00 is described below
commit 4a01e00a13323d232d66e9b4784cff91b5d992d1
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Tue Jun 8 00:49:51 2021 +0200
gnu: pigx-rnaseq: Update to 0.0.17.
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.17.
[arguments]: Remove "use-latest-salmon" phase; add "set-timezone" phase.
[inputs]: Replace r-gprofiler with r-gprofiler2; add r-ggpubr and
python-deeptools.
[native-inputs]: Add tzdata.
---
gnu/packages/bioinformatics.scm | 29 +++++++++++++++++------------
1 file changed, 17 insertions(+), 12 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 206c193..a4a6678 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10357,7 +10357,7 @@ once. This package provides tools to perform Drop-seq
analyses.")
(define-public pigx-rnaseq
(package
(name "pigx-rnaseq")
- (version "0.0.13")
+ (version "0.0.17")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/BIMSBbioinfo/pigx_rnaseq/"
@@ -10365,25 +10365,26 @@ once. This package provides tools to perform
Drop-seq analyses.")
"/pigx_rnaseq-" version ".tar.gz"))
(sha256
(base32
- "0z9zid2c8q16lfzlnjd63nparknhv31qgv4h79algmvhkakm2pgk"))))
+ "0k9zj50bij3sjwq08v8l8waddcx8k66m3vdq8mx5vc23p19qz42s"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-tests? #f ; not supported
#:phases
(modify-phases %standard-phases
- ;; See https://github.com/BIMSBbioinfo/pigx_rnaseq/issues/96
- (add-after 'unpack 'use-latest-salmon
- (lambda _
- (substitute* "snakefile.py"
- (("\"sa.bin\"") "\"pos.bin\""))
- (substitute* "tests/test_salmon/test_salmon_index.sh.in"
- (("sa.bin") "pos.bin"))))
- ;; "test.sh" runs STAR, which requires excessive amounts of memory.
+ ;; "test.sh" runs the whole pipeline, which takes a long time and
+ ;; might fail due to OOM. The MultiQC is also resource intensive.
(add-after 'unpack 'disable-resource-intensive-test
(lambda _
(substitute* "Makefile.in"
(("^ tests/test_multiqc/test.sh") "")
- (("^ test.sh") "")))))))
+ (("^ test.sh") ""))))
+ (add-before 'check 'set-timezone
+ ;; The readr package is picky about timezones.
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "TZ" "UTC+1")
+ (setenv "TZDIR"
+ (string-append (assoc-ref inputs "tzdata")
+ "/share/zoneinfo")))))))
(inputs
`(("coreutils" ,coreutils)
("sed" ,sed)
@@ -10398,8 +10399,9 @@ once. This package provides tools to perform Drop-seq
analyses.")
("r-minimal" ,r-minimal)
("r-rmarkdown" ,r-rmarkdown)
("r-ggplot2" ,r-ggplot2)
+ ("r-ggpubr" ,r-ggpubr)
("r-ggrepel" ,r-ggrepel)
- ("r-gprofiler" ,r-gprofiler)
+ ("r-gprofiler2" ,r-gprofiler2)
("r-deseq2" ,r-deseq2)
("r-dt" ,r-dt)
("r-knitr" ,r-knitr)
@@ -10417,7 +10419,10 @@ once. This package provides tools to perform Drop-seq
analyses.")
("pandoc" ,pandoc)
("pandoc-citeproc" ,pandoc-citeproc)
("python-wrapper" ,python-wrapper)
+ ("python-deeptools" ,python-deeptools)
("python-pyyaml" ,python-pyyaml)))
+ (native-inputs
+ `(("tzdata" ,tzdata)))
(home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipeline for RNA sequencing experiments")
(description "PiGX RNAseq is an analysis pipeline for preprocessing and
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