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| author | Marius Bakke <mbakke@fastmail.com> | 2020-05-05 20:43:21 +0200 |
|---|---|---|
| committer | Marius Bakke <mbakke@fastmail.com> | 2020-05-05 20:43:21 +0200 |
| commit | 87a40d7203a813921b3ef0805c2b46c0026d6c31 (patch) | |
| tree | cebad70c1df30969005c18c4d9faa39d7d80cbf6 /gnu/packages/bioinformatics.scm | |
| parent | ba151b7e1a9cc0baf932b5c5e0c916e54d2e27f4 (diff) | |
| parent | 751d1f01e4f0607d41e4c859d944753b18466652 (diff) | |
| download | patches-87a40d7203a813921b3ef0805c2b46c0026d6c31.tar patches-87a40d7203a813921b3ef0805c2b46c0026d6c31.tar.gz | |
Merge branch 'master' into core-updates
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 42 |
1 files changed, 42 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 617908a4a6..32b795948b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -79,6 +79,7 @@ #:use-module (gnu packages golang) #:use-module (gnu packages glib) #:use-module (gnu packages graph) + #:use-module (gnu packages graphviz) #:use-module (gnu packages groff) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) @@ -15854,3 +15855,44 @@ biological processes. SBML is useful for models of metabolism, cell signaling, and more. It continues to be evolved and expanded by an international community.") (license license:lgpl2.1+))) + +(define-public grocsvs + ;; The last release is out of date and new features have been added. + (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")) + (patches (search-patches "grocsvs-dont-use-admiral.patch")))) + (build-system python-build-system) + (arguments + `(#:tests? #f ; No test suite. + #:python ,python-2)) ; Only python-2 supported. + (inputs + `(("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)))) |