From 46264c73a6364e0510cbe6841a135da5d7f29dfa Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 16 Mar 2018 10:59:17 +0100
Subject: gnu: Add pigx-scrnaseq.

* gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable.
---
 gnu/packages/bioinformatics.scm | 77 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)

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")
-- 
cgit v1.2.3