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02/06: gnu: Add r-varianttools.
From: |
guix-commits |
Subject: |
02/06: gnu: Add r-varianttools. |
Date: |
Mon, 25 Mar 2019 11:20:17 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit c538bcdd38ca12fbdf02b220a371ac16448cab8c
Author: Ricardo Wurmus <address@hidden>
Date: Mon Mar 25 16:09:16 2019 +0100
gnu: Add r-varianttools.
* gnu/packages/bioconductor.scm (r-varianttools): New variable.
---
gnu/packages/bioconductor.scm | 40 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7bd126b..744fc87 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2579,3 +2579,43 @@ kernels, including: gkmSVM, kmer-SVM, mismatch kernel
and wildcard kernel.")
distributions of TF ChIP sequencing reads, taking advantage of an improved
peak definition in combination with known profile characteristics.")
(license license:gpl2)))
+
+(define-public r-varianttools
+ (package
+ (name "r-varianttools")
+ (version "1.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "VariantTools" version))
+ (sha256
+ (base32
+ "1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j"))))
+ (properties `((upstream-name . "VariantTools")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://bioconductor.org/packages/VariantTools/")
+ (synopsis "Tools for exploratory analysis of variant calls")
+ (description
+ "Explore, diagnose, and compare variant calls using filters. The
+VariantTools package supports a workflow for loading data, calling single
+sample variants and tumor-specific somatic mutations or other sample-specific
+variant types (e.g., RNA editing). Most of the functions operate on
+alignments (BAM files) or datasets of called variants. The user is expected
+to have already aligned the reads with a separate tool, e.g., GSNAP via
+gmapR.")
+ (license license:artistic2.0)))
- branch master updated (3080b81 -> a6d867f), guix-commits, 2019/03/25
- 03/06: gnu: Add r-heatplus., guix-commits, 2019/03/25
- 04/06: gnu: Add r-gosemsim., guix-commits, 2019/03/25
- 06/06: gnu: Add r-sigpathway., guix-commits, 2019/03/25
- 01/06: gnu: Add r-triform., guix-commits, 2019/03/25
- 02/06: gnu: Add r-varianttools.,
guix-commits <=
- 05/06: gnu: Add r-anota., guix-commits, 2019/03/25