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-rw-r--r--gnu/packages/bioinformatics.scm55
1 files changed, 55 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 744f8c2a4a..ca8dcb761a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -20,6 +20,7 @@
#: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 @@ that a read originated from a particular isoform.")
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")