diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 73 |
1 files changed, 70 insertions, 3 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 546b240f84..73765dafe7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10880,8 +10880,8 @@ memory usage and processing time is minimized.") (license license:expat))) (define-public r-dropbead - (let ((commit "cf0be5ae5302684bd03e78ab65b142900bbbb840") - (revision "1")) + (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") + (revision "2")) (package (name "r-dropbead") (version (string-append "0-" revision "." (string-take commit 7))) @@ -10894,7 +10894,7 @@ memory usage and processing time is minimized.") (file-name (git-file-name name version)) (sha256 (base32 - "1b2lphsc236s1rdzlijxg8yl1jnqpwcvj4x938r89rqpj93jb780")))) + "0sbzma49aiiyw8b0jpr7fnhzys9nsqmp4hy4hdz1gzyg1lhnca26")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -12646,3 +12646,70 @@ contains analyze RNA expression genome-wide in thousands of individual cells at once. This package provides tools to perform Drop-seq analyses.") (license license:expat))) + +(define-public pigx-rnaseq + (package + (name "pigx-rnaseq") + (version "0.0.2") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" + "releases/download/v" version + "/pigx_rnaseq-" version ".tar.gz")) + (sha256 + (base32 + "168hx2ig3rarphx3l21ay9yyg8ipaakzixnrhpbdi0sknhyvrrk8")))) + (build-system gnu-build-system) + (arguments + `(#:parallel-tests? #f ; not supported + #:phases + (modify-phases %standard-phases + (add-after 'install 'wrap-executable + ;; Make sure the executable finds all R modules. + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (wrap-program (string-append out "/bin/pigx-rnaseq") + `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) + `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) + #t))))) + (inputs + `(("snakemake" ,snakemake) + ("fastqc" ,fastqc) + ("multiqc" ,multiqc) + ("star" ,star) + ("trim-galore" ,trim-galore) + ("htseq" ,htseq) + ("samtools" ,samtools) + ("bedtools" ,bedtools) + ("r-minimal" ,r-minimal) + ("r-rmarkdown" ,r-rmarkdown) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-gprofiler" ,r-gprofiler) + ("r-deseq2" ,r-deseq2) + ("r-dt" ,r-dt) + ("r-knitr" ,r-knitr) + ("r-pheatmap" ,r-pheatmap) + ("r-corrplot" ,r-corrplot) + ("r-reshape2" ,r-reshape2) + ("r-plotly" ,r-plotly) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-crosstalk" ,r-crosstalk) + ("r-tximport" ,r-tximport) + ("r-rtracklayer" ,r-rtracklayer) + ("r-rjson" ,r-rjson) + ("salmon" ,salmon) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("python-wrapper" ,python-wrapper) + ("python-pyyaml" ,python-pyyaml))) + (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (synopsis "Analysis pipeline for RNA sequencing experiments") + (description "PiGX RNAseq is an analysis pipeline for preprocessing and +reporting for RNA sequencing experiments. It is easy to use and produces high +quality reports. The inputs are reads files from the sequencing experiment, +and a configuration file which describes the experiment. In addition to +quality control of the experiment, the pipeline produces a differential +expression report comparing samples in an easily configurable manner.") + (license license:gpl3+))) |