diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 35 |
1 files changed, 4 insertions, 31 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ce66ce0d37..34b843cfbb 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 (define-public python2-biopython (package-with-python2 python-biopython)) -;; An outdated version of biopython is required for seqmagick, see -;; https://github.com/fhcrc/seqmagick/issues/59 -;; When that issue has been resolved this package should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. @@ -5391,7 +5377,7 @@ 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) @@ -5400,25 +5386,12 @@ bioinformatics file formats, sequence alignment, and more.") version ".tar.gz")) (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 |