diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2021-06-07 11:35:27 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-06-07 16:50:33 +0200 |
| commit | 176513f5f3d09f9604a601fab7ba193e95a29c35 (patch) | |
| tree | 6e9a662eb912ba6c6780ac2394a6acf94d9e7016 | |
| parent | e3611cc412e7b1c750a56d17fb1b7cde684baa3f (diff) | |
gnu: jellyfish: Update to 2.3.0.
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.3.0.
[arguments]: Disable SSE to avoid tuning to the build node's CPU.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Update.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 17 |
1 files changed, 8 insertions, 9 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 788e7ae836..365a30c166 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4715,7 +4715,7 @@ experiments and provide highly stable thresholds based on reproducibility.") (define-public jellyfish (package (name "jellyfish") - (version "2.2.10") + (version "2.3.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/gmarcais/Jellyfish/" @@ -4723,14 +4723,15 @@ experiments and provide highly stable thresholds based on reproducibility.") "/jellyfish-" version ".tar.gz")) (sha256 (base32 - "1k4pc3fvv6w1km2yph4m5sd78fbxp21d6xyzgmy0gjihzc6mb249")))) + "0npa62wzasdibas5zp3n8j3armsci4kyvh0jw7jr0am4gg7vg5g1")))) (build-system gnu-build-system) (outputs '("out" ;for library "ruby" ;for Ruby bindings "python")) ;for Python bindings (arguments `(#:configure-flags - (list (string-append "--enable-ruby-binding=" + (list "--without-sse" ; configure script probes for CPU features when SSE is enabled. + (string-append "--enable-ruby-binding=" (assoc-ref %outputs "ruby")) (string-append "--enable-python-binding=" (assoc-ref %outputs "python"))) @@ -4740,13 +4741,12 @@ experiments and provide highly stable thresholds based on reproducibility.") (lambda _ ;; generator_manager.hpp either uses /bin/sh or $SHELL ;; to run tests. - (setenv "SHELL" (which "bash")) - #t))))) + (setenv "SHELL" (which "bash"))))))) (native-inputs `(("bc" ,bc) ("time" ,time) ("ruby" ,ruby) - ("python" ,python-2) + ("python" ,python-wrapper) ("pkg-config" ,pkg-config))) (inputs `(("htslib" ,htslib))) @@ -4762,9 +4762,8 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (home-page "http://www.genome.umd.edu/jellyfish.html") ;; JELLYFISH seems to be 64-bit only. (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux")) - ;; The combined work is published under the GPLv3 or later. Individual - ;; files such as lib/jsoncpp.cpp are released under the Expat license. - (license (list license:gpl3+ license:expat)))) + ;; One of these licenses may be picked + (license (list license:gpl3+ license:bsd-3)))) (define-public khmer (package |