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gnu: Add pbtranscript-tofu.

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* gnu/packages/bioinformatics.scm (pbtranscript-tofu): New variable.
This commit is contained in:
Ricardo Wurmus 2015-03-20 14:36:38 +01:00
parent ad641d53de
commit 2c16316ef4
1 changed files with 55 additions and 0 deletions
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55
gnu/packages/bioinformatics.scm
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@ -20,6 +20,7 @@ (define-module (gnu packages bioinformatics)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix build-system gnu)
#:use-module (guix build-system cmake)
#:use-module (guix build-system python)
@ -679,6 +680,60 @@ (define-public python2-pbcore
files and writing bioinformatics applications.")
(license license:bsd-3)))
(define-public pbtranscript-tofu
(let ((commit "c7bbd5472"))
(package
(name "pbtranscript-tofu")
(version (string-append "0.4.1." commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/PacificBiosciences/cDNA_primer.git")
(commit commit)))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"148xkzi689c49g6fdhckp6mnmj2qhjdf1j4wifm6ja7ij95d7fxx"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
;; With standard flags, the install phase attempts to create a zip'd
;; egg file, and fails with an error: 'ZIP does not support timestamps
;; before 1980'
#:configure-flags '("--single-version-externally-managed"
"--record=pbtranscript-tofu.txt")
#:phases
(alist-cons-after
'unpack 'enter-directory-and-clean-up
(lambda _
(chdir "pbtranscript-tofu/pbtranscript/")
;; Delete clutter
(delete-file-recursively "dist/")
(delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/")
(delete-file-recursively "pbtools.pbtranscript.egg-info")
(delete-file "Cython-0.20.1.tar.gz")
(delete-file "setuptools_cython-0.2.1-py2.7.egg")
(delete-file "setuptools_cython-0.2.1.tar.gz")
(delete-file "setup.cfg")
;; files should be writable for install phase
(for-each (lambda (f) (chmod f #o755))
(find-files "." "\\.py")))
%standard-phases)))
(inputs
`(("python-cython" ,python2-cython)
("python-numpy" ,python2-numpy)
("python-bx-python" ,python2-bx-python)
("python-pbcore" ,python2-pbcore)))
(native-inputs
`(("python-nose" ,python2-nose)
("python-setuptools" ,python2-setuptools)))
(home-page "https://github.com/PacificBiosciences/cDNA_primer")
(synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
(description
"pbtranscript-tofu contains scripts to analyze transcriptome data
generated using the PacBio Iso-Seq protocol.")
(license license:bsd-3))))
(define-public rseqc
(package
(name "rseqc")