diff options
| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-03-20 16:17:55 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-03-31 17:38:56 +0200 |
| commit | 8e913213d9d072ddf75c48b8db8f32b46d5a2a3c (patch) | |
| tree | 48fee003b092cb4040e9b215f48815226e77ace1 /gnu | |
| parent | 9af288a6805661627f964d9e9eae4518aaad266e (diff) | |
gnu: Add cutadapt.
* gnu/packages/bioinformatics.scm (cutadapt): New variable.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 41 |
1 files changed, 41 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ca8dcb761a..883eb19f6a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -19,6 +19,7 @@ (define-module (gnu packages bioinformatics) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) + #:use-module (guix utils) #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix build-system gnu) @@ -401,6 +402,46 @@ files between different genome assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") (license license:gpl2+))) +(define-public cutadapt + (package + (name "cutadapt") + (version "1.8") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/marcelm/cutadapt/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "161bp87y6gd6r5bmvjpn2b1k942i3fizfpa139f0jn6jv1wcp5h5")))) + (build-system python-build-system) + (arguments + ;; tests must be run after install + `(#:phases (alist-cons-after + 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (setenv "PYTHONPATH" + (string-append + (getenv "PYTHONPATH") + ":" (assoc-ref outputs "out") + "/lib/python" + (string-take (string-take-right + (assoc-ref inputs "python") 5) 3) + "/site-packages")) + (zero? (system* "nosetests" "-P" "tests"))) + (alist-delete 'check %standard-phases)))) + (native-inputs + `(("python-cython" ,python-cython) + ("python-nose" ,python-nose) + ("python-setuptools" ,python-setuptools))) + (home-page "https://code.google.com/p/cutadapt/") + (synopsis "Remove adapter sequences from nucleotide sequencing reads") + (description + "Cutadapt finds and removes adapter sequences, primers, poly-A tails and +other types of unwanted sequence from high-throughput sequencing reads.") + (license license:expat))) + (define-public flexbar (package (name "flexbar") |