@@ -3,7 +3,7 @@
;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2022 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016-2020, 2022 Marius Bakke <marius@gnu.org>
;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
@@ -35,6 +35,7 @@ (define-module (gnu packages python-science)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
#:use-module (gnu packages base)
+ #:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages cpp)
@@ -307,6 +308,54 @@ (define-public python-scikit-image
"Scikit-image is a collection of algorithms for image processing.")
(license license:bsd-3)))
+(define-public python-scikit-allel
+ (package
+ (name "python-scikit-allel")
+ (version "1.3.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "scikit-allel" version))
+ (sha256
+ (base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "python" "setup.py" "build_ext" "--inplace")
+ (invoke "python" "-m" "pytest" "-v" "allel"
+ ;; AttributeError: 'Dataset' object has no attribute 'asstr'
+ "-k" (string-append
+ "not test_vcf_to_hdf5"
+ " and not test_vcf_to_hdf5_exclude"
+ " and not test_vcf_to_hdf5_rename"
+ " and not test_vcf_to_hdf5_group"
+ " and not test_vcf_to_hdf5_ann"))))))))
+ (propagated-inputs
+ (list python-dask
+ python-numpy))
+ (native-inputs
+ (list python-cython
+ ;; The following are all needed for the tests
+ htslib
+ python-h5py
+ python-hmmlearn
+ python-numexpr
+ python-pytest
+ python-scipy
+ python-setuptools-scm
+ python-zarr))
+ (home-page "https://github.com/cggh/scikit-allel")
+ (synopsis "Explore and analyze genetic variation data")
+ (description
+ "This package provides utilities for exploratory analysis of large scale
+genetic variation data.")
+ (license license:expat)))
+
(define-public python-sgp4
(package
(name "python-sgp4")