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-rw-r--r--gn/packages/bioinformatics.scm40
1 files changed, 40 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 7e7f94d..177308b 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -14,6 +14,7 @@
#:use-module (guix build-system trivial)
#:use-module (guix build-system waf)
#:use-module (gnu packages)
+ #:use-module (gn packages python)
#:use-module (gnu packages bioconductor)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
@@ -1224,3 +1225,42 @@ here}.")
(synopsis "Efficient sequence alignment of full genomes")
(description "MUMmer is a versatil alignment tool for DNA and protein sequences.")
(license license:artistic2.0)))
+
+(define-public grocsvs
+ (let ((commit "ecd956a65093a0b2c41849050e4512d46fecea5d")
+ (revision "1"))
+ (package
+ (name "grocsvs")
+ (version (git-version "0.2.6.1" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/grocsvs/grocsvs")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "14505725gr7qxc17cxxf0k6lzcwmgi64pija4mwf29aw70qn35cc"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2)) ; Only python-2 supported.
+ (inputs
+ `(("python2-admiral" ,python2-admiral)
+ ("python2-h5py" ,python2-h5py)
+ ("python2-ipython-cluster-helper" ,python2-ipython-cluster-helper)
+ ("python2-networkx" ,python2-networkx)
+ ("python2-psutil" ,python2-psutil)
+ ("python2-pandas" ,python2-pandas)
+ ("python2-pybedtools" ,python2-pybedtools)
+ ("python2-pyfaidx" ,python2-pyfaidx)
+ ("python2-pygraphviz" ,python2-pygraphviz)
+ ("python2-pysam" ,python2-pysam)
+ ("python2-scipy" ,python2-scipy)))
+ (home-page "https://github.com/grocsvs/grocsvs")
+ (synopsis "Genome-wide reconstruction of complex structural variants")
+ (description
+ "@dfn{Genome-wide Reconstruction of Complex Structural Variants}
+(GROC-SVs), is a software pipeline for identifying large-scale structural
+variants, performing sequence assembly at the breakpoints, and reconstructing
+the complex structural variants using the long-fragment information from the
+10x Genomics platform.")
+ (license license:expat))))