diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 45 |
1 files changed, 8 insertions, 37 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0e9c20f1f1..d3b137513c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -790,20 +790,6 @@ into separate processes; and more.") (define-public python2-biopython (package-with-python2 python-biopython)) -;; An outdated version of biopython is required for seqmagick, see -;; https://github.com/fhcrc/seqmagick/issues/59 -;; When that issue has been resolved this package should be removed. -(define python2-biopython-1.66 - (package - (inherit python2-biopython) - (version "1.66") - (source (origin - (method url-fetch) - (uri (pypi-uri "biopython" version)) - (sha256 - (base32 - "1gdv92593klimg22icf5j9by7xiq86jnwzkpz4abaa05ylkdf6hp")))))) - (define-public bpp-core ;; The last release was in 2014 and the recommended way to install from source ;; is to clone the git repository, so we do this. @@ -3518,16 +3504,16 @@ sequencing tag position and orientation.") (define-public mafft (package (name "mafft") - (version "7.310") + (version "7.313") (source (origin (method url-fetch) (uri (string-append - "http://mafft.cbrc.jp/alignment/software/mafft-" version + "https://mafft.cbrc.jp/alignment/software/mafft-" version "-without-extensions-src.tgz")) (file-name (string-append name "-" version ".tgz")) (sha256 (base32 - "0gbsaz6z2qa307kd7wfb06c3y4ikmv1hsdvlns11f6zq4w1z9pwc")))) + "0r83qmg2if8mi6jyx3xdf8ar2gcxl7r9nmj98jr7lxym97v61a2k")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no automated tests, though there are tests in the read me @@ -5391,34 +5377,19 @@ bioinformatics file formats, sequence alignment, and more.") (define-public seqmagick (package (name "seqmagick") - (version "0.6.1") + (version "0.7.0") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/s/seqmagick/seqmagick-" - version ".tar.gz")) + (uri (pypi-uri "seqmagick" version)) (sha256 (base32 - "0cgn477n74gsl4qdaakrrhi953kcsd4q3ivk2lr18x74s3g4ma1d")))) + "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) (build-system python-build-system) - (arguments - ;; python2 only, see https://github.com/fhcrc/seqmagick/issues/56 - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - ;; Current test in setup.py does not work as of 0.6.1, - ;; so use nose to run tests instead for now. See - ;; https://github.com/fhcrc/seqmagick/issues/55 - (replace 'check (lambda _ (zero? (system* "nosetests"))))))) (inputs - ;; biopython-1.66 is required due to - ;; https://github.com/fhcrc/seqmagick/issues/59 - ;; When that issue is resolved the 'python2-biopython-1.66' package - ;; should be removed. - `(("python-biopython" ,python2-biopython-1.66))) + `(("python-biopython" ,python-biopython))) (native-inputs - `(("python-nose" ,python2-nose))) + `(("python-nose" ,python-nose))) (home-page "https://github.com/fhcrc/seqmagick") (synopsis "Tools for converting and modifying sequence files") (description |