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