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gnu: cutadapt: Update to 1.16.

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* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16.
[source]: Fetch via git.
[arguments]: Remove.
[native-inputs]: Replace python-nose with python-pytest.
This commit is contained in:
Ricardo Wurmus 2018-03-02 23:44:16 +01:00
parent 62a4b952c0
commit 3ede1550e8
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GPG key ID: 197A5888235FACAC
1 changed files with 8 additions and 24 deletions
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@ -1854,38 +1854,22 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
(define-public cutadapt (define-public cutadapt
(package (package
(name "cutadapt") (name "cutadapt")
(version "1.14") (version "1.16")
(source (origin (source (origin
(method url-fetch) (method git-fetch)
(uri (string-append (uri (git-reference
"https://github.com/marcelm/cutadapt/archive/v" (url "https://github.com/marcelm/cutadapt.git")
version ".tar.gz")) (commit (string-append "v" version))))
(file-name (string-append name "-" version ".tar.gz")) (file-name (string-append name "-" version "-checkout"))
(sha256 (sha256
(base32 (base32
"16gbpiwy4m48vq2h5wqar3i8vr6vcj9gcl2qvqim19x6ya9dp8kd")))) "09pr02067jiks19nc0aby4xp70hhgvb554i2y1c04rv1m401w7q8"))))
(build-system python-build-system) (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 (inputs
`(("python-xopen" ,python-xopen))) `(("python-xopen" ,python-xopen)))
(native-inputs (native-inputs
`(("python-cython" ,python-cython) `(("python-cython" ,python-cython)
("python-nose" ,python-nose))) ("python-pytest" ,python-pytest)))
(home-page "https://cutadapt.readthedocs.io/en/stable/") (home-page "https://cutadapt.readthedocs.io/en/stable/")
(synopsis "Remove adapter sequences from nucleotide sequencing reads") (synopsis "Remove adapter sequences from nucleotide sequencing reads")
(description (description