~ruther/guix-local

3ede1550e8310a8a544c1fb0f7f372c60c00bbe0 — Ricardo Wurmus 8 years ago 62a4b95 
gnu: cutadapt: Update to 1.16.

* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16.
[source]: Fetch via git.
[arguments]: Remove.
[native-inputs]: Replace python-nose with python-pytest.
patch browse .tar.gz 
1 files changed, 8 insertions(+), 24 deletions(-)

M gnu/packages/bioinformatics.scm

M gnu/packages/bioinformatics.scm => gnu/packages/bioinformatics.scm +8 -24
@@ 1854,38 1854,22 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
(define-public cutadapt
  (package
    (name "cutadapt")
    (version "1.14")
    (version "1.16")
    (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"))
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/marcelm/cutadapt.git")
                    (commit (string-append "v" version))))
              (file-name (string-append name "-" version "-checkout"))
              (sha256
               (base32
                "16gbpiwy4m48vq2h5wqar3i8vr6vcj9gcl2qvqim19x6ya9dp8kd"))))
                "09pr02067jiks19nc0aby4xp70hhgvb554i2y1c04rv1m401w7q8"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         ;; The tests must be run after installation.
         (delete 'check)
         (add-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")))))))
    (inputs
     `(("python-xopen" ,python-xopen)))
    (native-inputs
     `(("python-cython" ,python-cython)
       ("python-nose" ,python-nose)))
       ("python-pytest" ,python-pytest)))
    (home-page "https://cutadapt.readthedocs.io/en/stable/")
    (synopsis "Remove adapter sequences from nucleotide sequencing reads")
    (description