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-rw-r--r--gnu/packages/bioinformatics.scm77
1 files changed, 77 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 989e963c57..1b49cfdfbf 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12857,6 +12857,83 @@ and coverage and can be used to produce information on differential
methylation and segmentation.")
(license license:gpl3+)))
+(define-public pigx-scrnaseq
+ (package
+ (name "pigx-scrnaseq")
+ (version "0.0.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
+ "releases/download/v" version
+ "/pigx_scrnaseq-" version ".tar.gz"))
+ (sha256
+ (base32
+ "03gwp83823ji59y6nvyz89i4yd3faaqpc3791qia71i91470vfsg"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:configure-flags
+ (list (string-append "PICARDJAR=" (assoc-ref %build-inputs "java-picard")
+ "/share/java/picard.jar")
+ (string-append "DROPSEQJAR=" (assoc-ref %build-inputs "dropseq-tools")
+ "/share/java/dropseq.jar"))
+ #: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-scrnaseq")
+ `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
+ `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
+ #t)))))
+ (inputs
+ `(("dropseq-tools" ,dropseq-tools)
+ ("fastqc" ,fastqc)
+ ("java-picard" ,java-picard)
+ ("java" ,icedtea-8)
+ ("python-wrapper" ,python-wrapper)
+ ("python-pyyaml" ,python-pyyaml)
+ ("python-pandas" ,python-pandas)
+ ("python-numpy" ,python-numpy)
+ ("python-loompy" ,python-loompy)
+ ("ghc-pandoc" ,ghc-pandoc)
+ ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
+ ("snakemake" ,snakemake)
+ ("star" ,star)
+ ("r-minimal" ,r-minimal)
+ ("r-argparser" ,r-argparser)
+ ("r-cowplot" ,r-cowplot)
+ ("r-data-table" ,r-data-table)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+ ("r-dplyr" ,r-dplyr)
+ ("r-dropbead" ,r-dropbead)
+ ("r-dt" ,r-dt)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfiles" ,r-genomicfiles)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-hdf5array" ,r-hdf5array)
+ ("r-pheatmap" ,r-pheatmap)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-rtsne" ,r-rtsne)
+ ("r-scater" ,r-scater)
+ ("r-scran" ,r-scran)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-stringr" ,r-stringr)
+ ("r-yaml" ,r-yaml)))
+ (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+ (synopsis "Analysis pipeline for single-cell RNA sequencing experiments")
+ (description "PiGX scRNAseq is an analysis pipeline for preprocessing and
+quality control for single cell RNA sequencing experiments. The inputs are
+read files from the sequencing experiment, and a configuration file which
+describes the experiment. It produces processed files for downstream analysis
+and interactive quality reports. The pipeline is designed to work with UMI
+based methods.")
+ (license license:gpl3+)))
+
(define-public r-diversitree
(package
(name "r-diversitree")