From a98639d8aed1cbc5fb6423854f91ba4741ed5603 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Wed, 6 May 2020 11:58:01 +0300
Subject: gn: grocsvs upstreamed

---
 gn/packages/bioinformatics.scm | 39 ---------------------------------------
 1 file changed, 39 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 056bc3f..0678444 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -1141,45 +1141,6 @@ here}.")
     (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))))
-
 (define-public diagnostic-slider
   (let ((commit "514d65d4982133e4869e578c5553fced4c6d506c")
         (revision "1"))
-- 
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