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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.
master
Ricardo Wurmus 2021-06-07 11:35:27 +02:00
parent e3611cc412
commit 176513f5f3
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1 changed files with 8 additions and 9 deletions
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@ -4715,7 +4715,7 @@ experiments and provide highly stable thresholds based on reproducibility.")
(define-public jellyfish (define-public jellyfish
(package (package
(name "jellyfish") (name "jellyfish")
(version "2.2.10") (version "2.3.0")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append "https://github.com/gmarcais/Jellyfish/" (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")) "/jellyfish-" version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"1k4pc3fvv6w1km2yph4m5sd78fbxp21d6xyzgmy0gjihzc6mb249")))) "0npa62wzasdibas5zp3n8j3armsci4kyvh0jw7jr0am4gg7vg5g1"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(outputs '("out" ;for library (outputs '("out" ;for library
"ruby" ;for Ruby bindings "ruby" ;for Ruby bindings
"python")) ;for Python bindings "python")) ;for Python bindings
(arguments (arguments
`(#:configure-flags `(#: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")) (assoc-ref %outputs "ruby"))
(string-append "--enable-python-binding=" (string-append "--enable-python-binding="
(assoc-ref %outputs "python"))) (assoc-ref %outputs "python")))
@ -4740,13 +4741,12 @@ experiments and provide highly stable thresholds based on reproducibility.")
(lambda _ (lambda _
;; generator_manager.hpp either uses /bin/sh or $SHELL ;; generator_manager.hpp either uses /bin/sh or $SHELL
;; to run tests. ;; to run tests.
(setenv "SHELL" (which "bash")) (setenv "SHELL" (which "bash")))))))
#t)))))
(native-inputs (native-inputs
`(("bc" ,bc) `(("bc" ,bc)
("time" ,time) ("time" ,time)
("ruby" ,ruby) ("ruby" ,ruby)
("python" ,python-2) ("python" ,python-wrapper)
("pkg-config" ,pkg-config))) ("pkg-config" ,pkg-config)))
(inputs (inputs
`(("htslib" ,htslib))) `(("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") (home-page "http://www.genome.umd.edu/jellyfish.html")
;; JELLYFISH seems to be 64-bit only. ;; JELLYFISH seems to be 64-bit only.
(supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux")) (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
;; The combined work is published under the GPLv3 or later. Individual ;; One of these licenses may be picked
;; files such as lib/jsoncpp.cpp are released under the Expat license. (license (list license:gpl3+ license:bsd-3))))
(license (list license:gpl3+ license:expat))))
(define-public khmer (define-public khmer
(package (package