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authorBen Woodcroft <donttrustben@gmail.com>2016-04-24 21:59:02 +1000
committerBen Woodcroft <donttrustben@gmail.com>2016-08-06 09:44:28 +1000
commit9e12eba866d893b4a95577aebf0fc25b4ca2119f (patch)
tree87b8e0052c57416bbafcf22c2c515372f247e38c /gnu/packages/bioinformatics.scm
parentda4ac1aaa44ef6a68756fe35d15182c8228d6099 (diff)
gnu: Add python-biom-format.
* gnu/packages/bioinformatics.scm (python-biom-format, python2-biom-format): New variables.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm49
1 files changed, 49 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c3ba9634ba..80721b8797 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -380,6 +380,55 @@ pybedtools extends BEDTools by offering feature-level manipulations from with
Python.")
(license license:gpl2+)))
+(define-public python-biom-format
+ (package
+ (name "python-biom-format")
+ (version "2.1.5")
+ (source
+ (origin
+ (method url-fetch)
+ ;; Use GitHub as source because PyPI distribution does not contain
+ ;; test data: https://github.com/biocore/biom-format/issues/693
+ (uri (string-append "https://github.com/biocore/biom-format/archive/"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1n25w3p1rixbpac8iysmzcja6m4ip5r6sz19l8y6wlwi49hxn278"))))
+ (build-system python-build-system)
+ (inputs
+ `(("python-numpy" ,python-numpy)
+ ("python-scipy" ,python-scipy)
+ ("python-future" ,python-future)
+ ("python-click" ,python-click)
+ ("python-h5py" ,python-h5py)))
+ (home-page "http://www.biom-format.org")
+ (synopsis "Biological Observation Matrix (BIOM) format utilities")
+ (description
+ "The BIOM file format is designed to be a general-use format for
+representing counts of observations e.g. operational taxonomic units, KEGG
+orthology groups or lipid types, in one or more biological samples
+e.g. microbiome samples, genomes, metagenomes.")
+ (license license:bsd-3)
+ (properties `((python2-variant . ,(delay python2-biom-format))))))
+
+(define-public python2-biom-format
+ (let ((base (package-with-python2 (strip-python2-variant python-biom-format))))
+ (package
+ (inherit base)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ ;; Do not require the unmaintained pyqi library.
+ (add-after 'unpack 'remove-pyqi
+ (lambda _
+ (substitute* "setup.py"
+ (("install_requires.append\\(\"pyqi\"\\)") "pass"))
+ #t)))
+ ,@(package-arguments base)))
+ (native-inputs `(("python2-setuptools" ,python2-setuptools)
+ ,@(package-native-inputs base))))))
+
(define-public bioperl-minimal
(let* ((inputs `(("perl-module-build" ,perl-module-build)
("perl-data-stag" ,perl-data-stag)