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-rw-r--r--gnu/packages/bioinformatics.scm47
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