diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 58 |
1 files changed, 54 insertions, 4 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ac46fe4bcc..5fbfdf0b9b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1972,7 +1972,25 @@ trees (phylogenies) and characters.") (let ((base (package-with-python2 (strip-python2-variant python-dendropy)))) (package (inherit base) + ;; Do not use same source as 'python-dendropy' because the patched + ;; failing tests do not occur on Python 2. + (source + (origin + (method url-fetch) + (uri (pypi-uri "DendroPy" (package-version base))) + (sha256 + (base32 + "1jfz7gp18wph311w1yygbvjanb3n5mdqal439bb6myw41dwb5m63")))) + (arguments + `(#:python ,python-2 + #:phases + (modify-phases %standard-phases + (replace 'check + ;; There is currently a test failure that only happens on some + ;; systems, and only using "setup.py test" + (lambda _ (zero? (system* "nosetests"))))))) (native-inputs `(("python2-setuptools" ,python2-setuptools) + ("python2-nose" ,python2-nose) ,@(package-native-inputs base)))))) @@ -2019,7 +2037,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.8.22") + (version "0.8.23") (source (origin (method url-fetch) (uri (string-append @@ -2028,7 +2046,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0lbqa07c5z8pr4dvdrc14rqc4311kq69j1ldry9glfc8hg3x1kd1")))) + "0xpcq3fbk4c52xbpgyk5brl58rljvl83bg8nkxy8vs00pxanm7i2")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target @@ -5576,7 +5594,7 @@ track. The database is exposed as a @code{TxDb} object.") (define-public vsearch (package (name "vsearch") - (version "2.1.2") + (version "2.3.0") (source (origin (method url-fetch) @@ -5586,7 +5604,7 @@ track. The database is exposed as a @code{TxDb} object.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1zzfj6ydsfzljyswlwqknpp8s2cf31vimi1aqf9ljsbagjyizc58")) + "1r8fk3whkil348y5hfsd4r56qjmchhq4nxm6s7ra5rlisw0mf9fy")) (modules '((guix build utils))) (snippet '(begin @@ -6929,6 +6947,38 @@ elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-bsgenome-celegans-ucsc-ce10 + (package + (name "r-bsgenome-celegans-ucsc-ce10") + (version "1.4.0") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "http://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "BSgenome.Celegans.UCSC.ce10_" + version ".tar.gz")) + (sha256 + (base32 + "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) + (properties + `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) + (build-system r-build-system) + ;; As this package provides little more than a very large data file it + ;; doesn't make sense to build substitutes. + (arguments `(#:substitutable? #f)) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome))) + (home-page + "http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") + (synopsis "Full genome sequences for Worm") + (description + "This package provides full genome sequences for Caenorhabditis +elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings +objects.") + (license license:artistic2.0))) + (define-public r-bsgenome-dmelanogaster-ucsc-dm3 (package (name "r-bsgenome-dmelanogaster-ucsc-dm3") |