[PATCH 2/2] gnu: Add python-scikit-bio.

[Ben Woodcroft]

* 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