gnu: Remove grit.

* gnu/packages/bioinformatics.scm (grit): Delete variable.
This commit is contained in:
Maxim Cournoyer 2022-04-29 13:35:16 -04:00
parent 7963e12568
commit 9f4c958d62
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@ -4025,48 +4025,6 @@ (define-public gemma
genome-wide association studies}.")
(license license:gpl3)))
(define-public grit
(package
(name "grit")
(version "2.0.5")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/nboley/grit")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1l5v8vfvfbrpmgnrvbrbv40d0arhxcnmxgv2f1mlcqfa3q6bkqm9"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'generate-from-cython-sources
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Delete these C files to force fresh generation from pyx sources.
(delete-file "grit/sparsify_support_fns.c")
(delete-file "grit/call_peaks_support_fns.c")
(substitute* "setup.py"
(("Cython.Setup") "Cython.Build"))
#t)))))
(inputs
(list python2-scipy python2-numpy python2-pysam python2-networkx))
(native-inputs
(list python2-cython))
;; The canonical <http://grit-bio.org> home page times out as of 2020-01-21.
(home-page "https://github.com/nboley/grit")
(synopsis "Tool for integrative analysis of RNA-seq type assays")
(description
"GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
full length transcript models. When none of these data sources are available,
GRIT can be run by providing a candidate set of TES or TSS sites. In
addition, GRIT can merge in reference junctions and gene boundaries. GRIT can
also be run in quantification mode, where it uses a provided GTF file and just
estimates transcript expression.")
(license license:gpl3+)))
(define-public hisat
(package
(name "hisat")