diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 119 |
1 files changed, 119 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1214a0b708..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) @@ -285,6 +286,41 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.") (license license:gpl3+))) +(define-public python2-bx-python + (package + (name "python2-bx-python") + (version "0.7.2") + (source (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/b/bx-python/bx-python-" + version ".tar.gz")) + (sha256 + (base32 + "0ld49idhc5zjdvbhvjq1a2qmpjj7h5v58rqr25dzmfq7g34b50xh")) + (modules '((guix build utils))) + (snippet + '(substitute* "setup.py" + ;; remove dependency on outdated "distribute" module + (("^from distribute_setup import use_setuptools") "") + (("^use_setuptools\\(\\)") ""))))) + (build-system python-build-system) + (arguments + `(#:tests? #f ;tests fail because test data are not included + #:python ,python-2)) + (inputs + `(("python-numpy" ,python2-numpy) + ("zlib" ,zlib))) + (native-inputs + `(("python-nose" ,python2-nose) + ("python-setuptools" ,python2-setuptools))) + (home-page "http://bitbucket.org/james_taylor/bx-python/") + (synopsis "Tools for manipulating biological data") + (description + "bx-python provides tools for manipulating biological data, particularly +multiple sequence alignments.") + (license license:expat))) + (define-public clipper (package (name "clipper") @@ -615,6 +651,89 @@ RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform.") (license license:gpl2))) +(define-public python2-pbcore + (package + (name "python2-pbcore") + (version "0.9.3") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/PacificBiosciences/pbcore/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1z46rwjac93jm87cbj2zgjg6qvsgs65140wkbbxsvxps7ai4pm09")))) + (build-system python-build-system) + (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7 + (inputs + `(("python-cython" ,python2-cython) + ("python-numpy" ,python2-numpy) + ("python-pysam" ,python2-pysam) + ("python-h5py" ,python2-h5py))) + (native-inputs + `(("python-setuptools" ,python2-setuptools))) + (home-page "http://pacificbiosciences.github.io/pbcore/") + (synopsis "Library for reading and writing PacBio data files") + (description + "The pbcore package provides Python APIs for interacting with PacBio data +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") |