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| author | Efraim Flashner | 2020-03-12 02:24:05 -0500 |
|---|---|---|
| committer | Efraim Flashner | 2020-03-12 02:25:03 -0500 |
| commit | 99cbd15b00a71787257baaed86c1a3a0e23df137 (patch) | |
| tree | 88ad9d70db6007a5b51934a926019a276f50f3fc /gn/packages/bioinformatics.scm | |
| parent | 9f6b35cac5aa37bf3568b8525f17542d7e471eb6 (diff) | |
| download | guix-bioinformatics-99cbd15b00a71787257baaed86c1a3a0e23df137.tar.gz | |
gn: Add grocsvs and dependencies
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 40 |
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)))) |