diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 25 |
1 files changed, 6 insertions, 19 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 795b0f208e..6469e9e1a1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1894,31 +1894,18 @@ time.") (define-public crossmap (package (name "crossmap") - (version "0.2.1") + (version "0.2.9") (source (origin (method url-fetch) - (uri (string-append "mirror://sourceforge/crossmap/CrossMap-" - version ".tar.gz")) + (uri (pypi-uri "CrossMap" version)) (sha256 (base32 - "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f")) - ;; This patch has been sent upstream already and is available - ;; for download from Sourceforge, but it has not been merged. - (patches (search-patches "crossmap-allow-system-pysam.patch")) - (modules '((guix build utils))) - (snippet '(begin - ;; remove bundled copy of pysam - (delete-file-recursively "lib/pysam") - #t)))) + "1byhclrqnqpvc1rqkfh4jwj6yhn0x9y7jk47i0qcjlhk0pjkw92p")))) (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'set-env - (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1") #t))))) + (arguments `(#:python ,python-2)) (inputs - `(("python-numpy" ,python2-numpy) + `(("python-bx-python" ,python2-bx-python) + ("python-numpy" ,python2-numpy) ("python-pysam" ,python2-pysam) ("zlib" ,zlib))) (native-inputs |