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authorRicardo Wurmus <rekado@elephly.net>2022-04-05 17:26:53 +0200
committerRicardo Wurmus <rekado@elephly.net>2022-04-05 18:40:48 +0200
commite721122069528b38e9dc901c4ca69acba0df5aea (patch)
treecb1f1d669720f88c030b34bfb006a61d00379418 /gnu
parent5d1c9fcdcf81bb95516f2d44e293c760300c9589 (diff)
gnu: pigx-scrnaseq: Use new inputs style.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use plain list.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm85
1 files changed, 43 insertions, 42 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3ad8800fdb..5ca1104436 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11149,50 +11149,51 @@ methylation and segmentation.")
(lambda _
(setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))))))
(inputs
- `(("coreutils" ,coreutils)
- ("perl" ,perl)
- ("fastqc" ,fastqc)
- ("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)
- ("pandoc" ,pandoc)
- ("samtools" ,samtools)
- ("snakemake" ,snakemake)
- ("star" ,star-for-pigx)
- ("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-seurat" ,r-seurat)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-stringr" ,r-stringr)
- ("r-yaml" ,r-yaml)))
+ (list coreutils
+ perl
+ fastqc
+ flexbar
+ icedtea-8
+ jellyfish
+ python-wrapper
+ python-pyyaml
+ python-pandas
+ python-magic
+ python-numpy
+ python-loompy
+ pandoc
+ samtools
+ snakemake
+ star-for-pigx
+ r-minimal
+ r-argparser
+ r-cowplot
+ r-data-table
+ r-delayedarray
+ r-delayedmatrixstats
+ r-dplyr
+ r-dropbead
+ r-dt
+ r-genomicalignments
+ r-genomicfiles
+ r-genomicranges
+ r-ggplot2
+ r-hdf5array
+ r-pheatmap
+ r-rmarkdown
+ r-rsamtools
+ r-rtracklayer
+ r-rtsne
+ r-scater
+ r-scran
+ r-seurat
+ r-singlecellexperiment
+ r-stringr
+ r-yaml))
(home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipeline for single-cell RNA sequencing experiments")
- (description "PiGX scRNAseq is an analysis pipeline for preprocessing and
+ (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