summaryrefslogtreecommitdiff
path: root/gnu/packages
diff options
context:
space:
mode:
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioinformatics.scm17
1 files changed, 6 insertions, 11 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 753b7fd0f5..e64842b9d6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12770,7 +12770,7 @@ methylation and segmentation.")
(define-public pigx-scrnaseq
(package
(name "pigx-scrnaseq")
- (version "0.0.8")
+ (version "1.1.3")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
@@ -12778,27 +12778,21 @@ methylation and segmentation.")
"/pigx_scrnaseq-" version ".tar.gz"))
(sha256
(base32
- "0zv0sc5amivxhb95vx2gfx6l9bh7n80fh7h47dalnwxxnfvnzai4"))))
+ "0ga2jr4968qzwml6aycky4603q64lny3y7lzw6dmafch5pydl1qi"))))
(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"))))
(inputs
`(("coreutils" ,coreutils)
("perl" ,perl)
- ("dropseq-tools" ,dropseq-tools)
("fastqc" ,fastqc)
- ("java-picard" ,java-picard-2.10.3) ; same as for dropseq
+ ("flexbar" ,flexbar)
("java" ,icedtea-8)
+ ("jellyfish" ,jellyfish)
("python-wrapper" ,python-wrapper)
("python-pyyaml" ,python-pyyaml)
("python-pandas" ,python-pandas)
("python-magic" ,python-magic)
("python-numpy" ,python-numpy)
- ("python-loompy" ,python-loompy-for-pigx-scrnaseq)
+ ("python-loompy" ,python-loompy)
("ghc-pandoc" ,ghc-pandoc)
("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
("samtools" ,samtools)
@@ -12825,6 +12819,7 @@ methylation and segmentation.")
("r-rtsne" ,r-rtsne)
("r-scater" ,r-scater)
("r-scran" ,r-scran)
+ ("r-seurat" ,r-seurat)
("r-singlecellexperiment" ,r-singlecellexperiment)
("r-stringr" ,r-stringr)
("r-yaml" ,r-yaml)))