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gnu: bioruby: Update to 2.0.4.

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* gnu/packages/bioinformatics.scm (bioruby): Update to 2.0.4.
[arguments]: Update style.
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Christopher Baines 2023-06-18 12:17:53 +01:00
parent 6bafbfd40f
commit 7b535eb29b
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1 changed files with 16 additions and 16 deletions
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gnu/packages/bioinformatics.scm
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@ -10876,34 +10876,34 @@ generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.")
(define-public bioruby (define-public bioruby
(package (package
(name "bioruby") (name "bioruby")
(version "1.5.2") (version "2.0.4")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
(uri (rubygems-uri "bio" version)) (uri (rubygems-uri "bio" version))
(sha256 (sha256
(base32 (base32
"1d56amdsjv1mag7m6gv2w0xij8hqx1v5xbdjsix8sp3yp36m7938")))) "08aknxk2ingwscwfqpw5vnax6jpk1sxfaialravladb63hcl8dx9"))))
(build-system ruby-build-system) (build-system ruby-build-system)
(propagated-inputs (propagated-inputs
(list ruby-libxml)) (list ruby-libxml))
(native-inputs (native-inputs
(list which)) ; required for test phase (list which)) ; required for test phase
(arguments (arguments
`(#:phases (list
(modify-phases %standard-phases #:phases
(add-before 'build 'patch-test-command #~(modify-phases %standard-phases
(lambda _ (add-before 'build 'patch-test-command
(substitute* '("test/functional/bio/test_command.rb") (lambda _
(("/bin/sh") (which "sh"))) (substitute* '("test/functional/bio/test_command.rb")
(substitute* '("test/functional/bio/test_command.rb") (("/bin/sh") (which "sh")))
(("/bin/ls") (which "ls"))) (substitute* '("test/functional/bio/test_command.rb")
(substitute* '("test/functional/bio/test_command.rb") (("/bin/ls") (which "ls")))
(("which") (which "which"))) (substitute* '("test/functional/bio/test_command.rb")
(substitute* '("test/functional/bio/test_command.rb", (("which") (which "which")))
"test/data/command/echoarg2.sh") (substitute* '("test/functional/bio/test_command.rb"
(("/bin/echo") (which "echo"))) "test/data/command/echoarg2.sh")
#t))))) (("/bin/echo") (which "echo"))))))))
(synopsis "Ruby library, shell and utilities for bioinformatics") (synopsis "Ruby library, shell and utilities for bioinformatics")
(description "BioRuby comes with a comprehensive set of Ruby development (description "BioRuby comes with a comprehensive set of Ruby development
tools and libraries for bioinformatics and molecular biology. BioRuby has tools and libraries for bioinformatics and molecular biology. BioRuby has