diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 47 |
1 files changed, 20 insertions, 27 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a448b51c6c..7bf39c6b03 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net> -;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com> +;;; Copyright © 2015, 2016, 2017 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> @@ -238,7 +238,7 @@ instance, it implements several methods to assess contig-wise read coverage.") (define-public bamtools (package (name "bamtools") - (version "2.3.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (string-append @@ -247,7 +247,7 @@ instance, it implements several methods to assess contig-wise read coverage.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1brry29bw2xr2l9pqn240rkqwayg85b8qq78zk2zs6nlspk4d018")))) + "0jr024kcrhjb82cm69i7p5fcg5375zlc1h3qh2n1v368hcd0qflk")))) (build-system cmake-build-system) (arguments `(#:tests? #f ;no "check" target @@ -499,6 +499,9 @@ provides the Ribotaper pipeline.") ("python-matplotlib" ,python2-matplotlib) ("python-scipy" ,python2-scipy) ("python-statsmodels" ,python2-statsmodels))) + (native-inputs + `(("python-mock" ,python2-mock) + ("python-nose" ,python2-nose))) (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/") (synopsis "Detect translation efficiency changes from ribosome footprints") (description "RiboDiff is a statistical tool that detects the protein @@ -604,6 +607,8 @@ Python.") ("python-future" ,python-future) ("python-click" ,python-click) ("python-h5py" ,python-h5py))) + (native-inputs + `(("python-nose" ,python-nose))) (home-page "http://www.biom-format.org") (synopsis "Biological Observation Matrix (BIOM) format utilities") (description @@ -1602,6 +1607,7 @@ databases.") ("python-scipy" ,python2-scipy))) (native-inputs `(("python-mock" ,python2-mock) ; for tests + ("python-nose" ,python2-nose) ; for tests ("python-pytz" ,python2-pytz))) ; for tests (home-page "https://github.com/YeoLab/clipper") (synopsis "CLIP peak enrichment recognition") @@ -1978,7 +1984,8 @@ accessing bigWig files.") (uri (pypi-uri "DendroPy" version)) (sha256 (base32 - "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p")))) + "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p")) + (patches (search-patches "python-dendropy-fix-tests.patch")))) (build-system python-build-system) (home-page "http://packages.python.org/DendroPy/") (synopsis "Library for phylogenetics and phylogenetic computing") @@ -2030,6 +2037,7 @@ trees (phylogenies) and characters.") ("python-pybigwig" ,python2-pybigwig))) (native-inputs `(("python-mock" ,python2-mock) ;for tests + ("python-nose" ,python2-nose) ;for tests ("python-pytz" ,python2-pytz))) ;for tests (home-page "https://github.com/fidelram/deepTools") (synopsis "Tools for normalizing and visualizing deep-sequencing data") @@ -2047,7 +2055,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.8.34") + (version "0.8.36") (source (origin (method url-fetch) (uri (string-append @@ -2056,7 +2064,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0jvr34g346gbz7z1zb9bs0vplivm9p4cxk0lbzklvdpa7g236p39")))) + "092smzzjcg51n3x4h84k52ijpz9m40ri838j9k2i463ribc3c8rh")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target @@ -2969,28 +2977,10 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r")))) (build-system python-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after - 'install 'wrap-program - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (python-version (string-take (string-take-right - (assoc-ref inputs "python") 5) 3)) - (path (string-join - (map (lambda (name) - (string-append (assoc-ref inputs name) - "/lib/python" python-version - "/site-packages")) - '("python-scipy" - "python-numpy" - "python-matplotlib")) - ":"))) - (wrap-program (string-append out "/bin/idr") - `("PYTHONPATH" ":" prefix (,path)))) - #t))))) - (inputs + `(#:tests? #f)) ; FIXME: "ImportError: No module named 'utility'" + (propagated-inputs `(("python-scipy" ,python-scipy) + ("python-sympy" ,python-sympy) ("python-numpy" ,python-numpy) ("python-matplotlib" ,python-matplotlib))) (native-inputs @@ -3679,6 +3669,9 @@ the phenotype as it models the data.") (build-system python-build-system) (arguments `(#:python ,python-2 + ;; FIXME: Tests fail with "No such file or directory: + ;; pbtools/pbtranscript/modified_bx_intervals/intersection_unique.so" + #:tests? #f #:phases (modify-phases %standard-phases (add-after 'unpack 'enter-directory |