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-rw-r--r--gnu/packages/bioinformatics.scm83
1 files changed, 28 insertions, 55 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9afb2c1197..9163b5dc8a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3742,75 +3742,48 @@ command, or queried for specific k-mers with @code{jellyfish query}.")
(define-public khmer
(package
(name "khmer")
- (version "2.0")
+ (version "2.1.2")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "khmer" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dib-lab/khmer.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0wb05shqh77v00256qlm68vbbx3kl76fyzihszbz5nhanl4ni33a"))
- (patches (search-patches "khmer-use-libraries.patch"))))
+ "02x38d9jw2r58y8dmnj4hffy9wxv1yc1jwbvdbhby9dxndv94r9m"))
+ (patches (search-patches "khmer-use-libraries.patch"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete bundled libraries. We do not replace the bundled seqan
+ ;; as it is a modified subset of the old version 1.4.1.
+ ;;
+ ;; We do not replace the bundled MurmurHash as the canonical
+ ;; repository for this code 'SMHasher' is unsuitable for providing
+ ;; a library. See
+ ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html
+ (delete-file-recursively "third-party/zlib")
+ (delete-file-recursively "third-party/bzip2")
+ #t))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
- (add-after 'unpack 'set-paths
- (lambda* (#:key inputs outputs #:allow-other-keys)
- ;; Delete bundled libraries.
- (delete-file-recursively "third-party/zlib")
- (delete-file-recursively "third-party/bzip2")
- ;; Replace bundled seqan.
- (let* ((seqan-all "third-party/seqan")
- (seqan-include (string-append
- seqan-all "/core/include")))
- (delete-file-recursively seqan-all)
- (copy-recursively (string-append (assoc-ref inputs "seqan")
- "/include/seqan")
- (string-append seqan-include "/seqan")))
- ;; We do not replace the bundled MurmurHash as the canonical
- ;; repository for this code 'SMHasher' is unsuitable for
- ;; providing a library. See
- ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html
- #t))
(add-after 'unpack 'set-cc
- (lambda _
- (setenv "CC" "gcc")
- #t))
- ;; It is simpler to test after installation.
- (delete 'check)
- (add-after 'install 'post-install-check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (setenv "PATH"
- (string-append
- (getenv "PATH")
- ":"
- (assoc-ref outputs "out")
- "/bin"))
- (setenv "PYTHONPATH"
- (string-append
- (getenv "PYTHONPATH")
- ":"
- out
- "/lib/python"
- (string-take (string-take-right
- (assoc-ref inputs "python") 5) 3)
- "/site-packages"))
- (with-directory-excursion "build"
- (zero? (system* "nosetests" "khmer" "--attr"
- "!known_failing")))))))))
+ (lambda _ (setenv "CC" "gcc") #t))
+ ;; FIXME: This fails with "permission denied".
+ (delete 'reset-gzip-timestamps))))
(native-inputs
- `(("seqan" ,seqan)
- ("python-nose" ,python-nose)))
+ `(("python-cython" ,python-cython)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-runner" ,python-pytest-runner)))
(inputs
`(("zlib" ,zlib)
("bzip2" ,bzip2)
("python-screed" ,python-screed)
- ("python-bz2file" ,python-bz2file)
- ;; Tests fail when gcc-5 is used for compilation. Use gcc-4.9 at least
- ;; until the next version of khmer (likely 2.1) is released.
- ("gcc" ,gcc-4.9)))
+ ("python-bz2file" ,python-bz2file)))
(home-page "https://khmer.readthedocs.org/")
(synopsis "K-mer counting, filtering and graph traversal library")
(description "The khmer software is a set of command-line tools for