* gnu/packages/python.scm (python-scikit-bio, python2-scikit-bio):
New variables.
---
gnu/packages/bioinformatics.scm | 84 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 84 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 899ce1c..fa67f3b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3339,6 +3339,90 @@ optimize the sequencing depth, or to screen multiple
libraries to avoid low
complexity samples.")
(license license:gpl3+)))
+(define-public python-scikit-bio
+ (package
+ (name "python-scikit-bio")
+ (version "0.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "scikit-bio" version))
+ (sha256
+ (base32
+ "06nrcgfz6c3jb2dnaf1wnvx3dyww94p454c4126gvcvfgv6scczy"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ ;; Install procedure installs extraneous binaries.
+ (add-after 'install 'remove-extraneous-files
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (delete-file-recursively bin))
+ #t))
+ ;; Tests are intended to be run using 'make test' not 'setup.py
+ ;; test', but there are many test failures anyway
+ ;; e.g. https://github.com/biocore/scikit-bio/issues/1308. Run a
+ ;; simple import test instead.
+ (delete 'check)
+ (add-after 'install 'check-after-install
+ (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?
+ (with-directory-excursion "ci"
+ (system*
+ "python"
+ "-c"
+ (string-append "import matplotlib; "
+ "matplotlib.use(\"Agg\"); "
+ "import skbio")))))))))
+ (native-inputs
+ `(("python-nose" ,python-nose)
+ ("python-pep8" ,python-pep8)
+ ("python-flake8" ,python-flake8)
+ ("python-dateutil" ,python-dateutil-2)))
+ (propagated-inputs
+ `(("python-bz2file" ,python-bz2file)
+ ("python-lockfile" ,python-lockfile)
+ ("python-cachecontrol" ,python-cachecontrol)
+ ("python-contextlib2" ,python-contextlib2)
+ ("python-decorator" ,python-decorator)
+ ("python-future" ,python-future)
+ ("python-ipython" ,python-ipython)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-natsort" ,python-natsort)
+ ("python-numpy" ,python-numpy)
+ ("python-pandas" ,python-pandas)
+ ("python-scipy" ,python-scipy)
+ ("python-six" ,python-six)))
+ (home-page "http://scikit-bio.org";)
+ (synopsis "Resources for bioinformatics")
+ (description
+ "Scikit-bio is a library for working with biological data in Python,
+providing data structures, algorithms and educational resources. It defines
+Python packages for biological sequences, alignments, tree, visualisation,
+diversity calculation and file I/O.")
+ (license license:bsd-3)
+ (properties `((python2-variant . ,(delay python2-scikit-bio))))))
+
+(define-public python2-scikit-bio
+ (let ((base (package-with-python2
+ (strip-python2-variant python-scikit-bio))))
+ (package
+ (inherit base)
+ (native-inputs
+ (append (package-native-inputs base)
+ `(("python2-setuptools" ,python2-setuptools)
+ ("python2-mock" ,python2-mock)))))))
+
(define-public sra-tools
(package
(name "sra-tools")
--
2.5.0
