@@ 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")