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gnu: bowtie: Update to 2.3.4.3.

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* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.4.3.
[source]: Fetch from git.
[inputs]: Replace python-2 with python-wrapper; move perl, perl-clone,
perl-test-deep, and perl-test-simple from here...
[native-inputs]: ...to here.
[arguments]: Simplify check phase.
This commit is contained in:
Ricardo Wurmus 2018-10-20 23:04:02 +02:00
parent f45093429c
commit 21c837405a
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GPG key ID: 197A5888235FACAC
1 changed files with 22 additions and 19 deletions
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gnu/packages/bioinformatics.scm
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@ -1273,15 +1273,16 @@ errors at the end of reads.")
(define-public bowtie (define-public bowtie
(package (package
(name "bowtie") (name "bowtie")
(version "2.3.2") (version "2.3.4.3")
(source (origin (source (origin
(method url-fetch) (method git-fetch)
(uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v" (uri (git-reference
version ".tar.gz")) (url "https://github.com/BenLangmead/bowtie2.git")
(file-name (string-append name "-" version ".tar.gz")) (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90")) "1zl3cf327y2p7p03cavymbh7b00djc7lncfaqih33n96iy9q8ibp"))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet (snippet
'(begin '(begin
@ -1291,14 +1292,6 @@ errors at the end of reads.")
(("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")) (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
#t)))) #t))))
(build-system gnu-build-system) (build-system gnu-build-system)
(inputs
`(("perl" ,perl)
("perl-clone" ,perl-clone)
("perl-test-deep" ,perl-test-deep)
("perl-test-simple" ,perl-test-simple)
("python" ,python-2)
("tbb" ,tbb)
("zlib" ,zlib)))
(arguments (arguments
'(#:make-flags '(#:make-flags
(list "allall" (list "allall"
@ -1308,11 +1301,21 @@ errors at the end of reads.")
(modify-phases %standard-phases (modify-phases %standard-phases
(delete 'configure) (delete 'configure)
(replace 'check (replace 'check
(lambda* (#:key outputs #:allow-other-keys) (lambda _
(zero? (system* "perl" (invoke "perl"
"scripts/test/simple_tests.pl" "scripts/test/simple_tests.pl"
"--bowtie2=./bowtie2" "--bowtie2=./bowtie2"
"--bowtie2-build=./bowtie2-build"))))))) "--bowtie2-build=./bowtie2-build")
#t)))))
(inputs
`(("tbb" ,tbb)
("zlib" ,zlib)
("python" ,python-wrapper)))
(native-inputs
`(("perl" ,perl)
("perl-clone" ,perl-clone)
("perl-test-deep" ,perl-test-deep)
("perl-test-simple" ,perl-test-simple)))
(home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml") (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
(synopsis "Fast and sensitive nucleotide sequence read aligner") (synopsis "Fast and sensitive nucleotide sequence read aligner")
(description (description