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| author | Ricardo Wurmus <rekado@elephly.net> | 2020-08-16 15:56:22 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2020-08-16 15:57:27 +0200 |
| commit | 4d55432fd02279b205097b54c88e3479daba29f5 (patch) | |
| tree | f76c0db888d8fca69b5cf7df28d71b76f957d1af /gnu/packages/bioinformatics.scm | |
| parent | 6f5530b9bc3b3fcf6958ed3854d361f38d095a95 (diff) | |
| download | guix-patches-4d55432fd02279b205097b54c88e3479daba29f5.tar guix-patches-4d55432fd02279b205097b54c88e3479daba29f5.tar.gz | |
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.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 16 |
1 files changed, 12 insertions, 4 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4c89aa4ef2..4a984bee60 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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") |