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gnu: pigx-bsseq: Update to 0.1.2.

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* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.2.
[inputs]: Add r-ggrepel, bwa-meth, methyldackel, multiqc, and samblaster.
This commit is contained in:
Ricardo Wurmus 2020-08-16 15:56:22 +02:00
parent 6f5530b9bc
commit 4d55432fd0
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1 changed files with 12 additions and 4 deletions
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gnu/packages/bioinformatics.scm
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@ -13040,7 +13040,7 @@ in an easily configurable manner.")
(define-public pigx-bsseq
(package
(name "pigx-bsseq")
(version "0.0.10")
(version "0.1.2")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
@ -13048,10 +13048,13 @@ in an easily configurable manner.")
"/pigx_bsseq-" version ".tar.gz"))
(sha256
(base32
"0l97wvkq4diq8lcarraj33bby1zzf0w804jwi8mlc5qddp8idwhy"))))
"0mpzlay2d5cjpmrcp7knff6rg1c2mqszd638n7lw0mc0cycbp9f8"))))
(build-system gnu-build-system)
(arguments
`(#:phases
`(;; TODO: tests currently require 12+GB of RAM. See
;; https://github.com/BIMSBbioinfo/pigx_bsseq/issues/164
#:tests? #f
#:phases
(modify-phases %standard-phases
(add-before 'check 'set-timezone
;; The readr package is picky about timezones.
@ -13071,6 +13074,7 @@ in an easily configurable manner.")
("r-annotationhub" ,r-annotationhub)
("r-dt" ,r-dt)
("r-genomation" ,r-genomation)
("r-ggrepel" ,r-ggrepel)
("r-methylkit" ,r-methylkit)
("r-rtracklayer" ,r-rtracklayer)
("r-rmarkdown" ,r-rmarkdown)
@ -13083,10 +13087,14 @@ in an easily configurable manner.")
("python-pyyaml" ,python-pyyaml)
("snakemake" ,snakemake)
("bismark" ,bismark)
("fastqc" ,fastqc)
("bowtie" ,bowtie)
("bwa-meth" ,bwa-meth)
("fastqc" ,fastqc)
("methyldackel" ,methyldackel)
("multiqc" ,multiqc)
("trim-galore" ,trim-galore)
("cutadapt" ,cutadapt)
("samblaster" ,samblaster)
("samtools" ,samtools)))
(home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")