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.
This commit is contained in:
Ricardo Wurmus 2021-06-07 11:35:27 +02:00
parent e3611cc412
commit 176513f5f3
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@ -4715,7 +4715,7 @@ (define-public idr
(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 @@ (define-public jellyfish
"/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 @@ (define-public jellyfish
(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 @@ (define-public jellyfish
(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