diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 46 |
1 files changed, 9 insertions, 37 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8c01386821..6be9694080 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -983,16 +983,17 @@ e.g. microbiome samples, genomes, metagenomes.") (version "1.7.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/bioperl/bioperl-live/" - "archive/release-" - (string-map (lambda (c) - (if (char=? c #\.) - #\- c)) version) - ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/bioperl/bioperl-live") + (commit (string-append "release-" + (string-map (lambda (c) + (if (char=? c #\.) + #\- c)) version))))) + (file-name (git-file-name name version)) (sha256 (base32 - "12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06")))) + "0wl8yvzcls59pwwk6m8ahy87pwg6nnibzy5cldbvmcwg2x2w7783")))) (build-system perl-build-system) (arguments `(#:phases @@ -11572,35 +11573,6 @@ provide this functionality without the necessity of drawing in a heavy-weight dependency like SeqAn.") (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt")))) -(define-public libdivsufsort - (package - (name "libdivsufsort") - (version "2.0.1") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/y-256/libdivsufsort.git") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2")))) - (build-system cmake-build-system) - (arguments - '(#:tests? #f ; there are no tests - #:configure-flags - ;; Needed for rapmap and sailfish. - '("-DBUILD_DIVSUFSORT64=ON"))) - (home-page "https://github.com/y-256/libdivsufsort") - (synopsis "Lightweight suffix-sorting library") - (description "libdivsufsort is a software library that implements a -lightweight suffix array construction algorithm. This library provides a -simple and an efficient C API to construct a suffix array and a -Burrows-Wheeler transformed string from a given string over a constant-size -alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1) -bytes of memory space, where n is the length of the string.") - (license license:expat))) - (define-public sailfish (package (name "sailfish") |