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| author | Ricardo Wurmus <rekado@elephly.net> | 2018-03-02 23:44:16 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2018-03-02 23:44:16 +0100 |
| commit | 3ede1550e8310a8a544c1fb0f7f372c60c00bbe0 (patch) | |
| tree | b3abb524b04031dcc452c67aee1643e987b2b295 /gnu | |
| parent | 62a4b952c041d5643f1a1ef05450dd8fb59e9bbf (diff) | |
| download | patches-3ede1550e8310a8a544c1fb0f7f372c60c00bbe0.tar patches-3ede1550e8310a8a544c1fb0f7f372c60c00bbe0.tar.gz | |
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.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 32 |
1 files changed, 8 insertions, 24 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e5e9192993..e13f1b369f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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 |