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gnu: pigx-rnaseq: Update to 0.0.17.

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* 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.
This commit is contained in:
Ricardo Wurmus 2021-06-08 00:49:51 +02:00
parent fc58d9ac66
commit 4a01e00a13
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GPG key ID: 197A5888235FACAC
1 changed files with 17 additions and 12 deletions
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@ -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