diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 55 |
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") |