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-rw-r--r--gnu/packages/bioinformatics.scm25
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