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gnu: kaiju: Update to 1.9.0.

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* gnu/packages/bioinformatics.scm (kaiju): Update to 1.9.0.
[arguments]: Use gexps; wrap scripts in install phase.
[inputs]: Add bzip2, coreutils, curl, gawk, guile-3.0, gzip,
python-wrapper, tar, and wget.
This commit is contained in:
Ricardo Wurmus 2022-10-04 23:07:19 +02:00
parent a96ebe47b0
commit 9ed65e6af7
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GPG key ID: 197A5888235FACAC
1 changed files with 37 additions and 16 deletions
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gnu/packages/bioinformatics.scm
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@ -4845,7 +4845,7 @@ (define-public khmer
(define-public kaiju
(package
(name "kaiju")
(version "1.6.3")
(version "1.9.0")
(source (origin
(method git-fetch)
(uri (git-reference
@ -4854,24 +4854,45 @@ (define-public kaiju
(file-name (git-file-name name version))
(sha256
(base32
"119pzi0ddzv9mjg4wwa6han0cwr3k3ssn7kirvsjfcq05mi5ka0x"))))
"1hfmadkfs6jjd7l3byly5xxb0ifm3dm1wis11sjbqfcv6l89snmg"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; There are no tests.
#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-before 'build 'move-to-src-dir
(lambda _ (chdir "src") #t))
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(mkdir-p bin)
(chdir "..")
(copy-recursively "bin" bin))
#t)))))
(list
#:tests? #f ; There are no tests.
#:phases
#~(modify-phases %standard-phases
(delete 'configure)
(add-before 'build 'move-to-src-dir
(lambda _ (chdir "src")))
(replace 'install
(lambda _
(let ((bin (string-append #$output "/bin")))
(mkdir-p bin)
(copy-recursively "../bin" bin)
(let ((path (search-path-as-list '("bin")
'#$(match (package-inputs this-package)
(((_ pkg) ...) pkg)))))
(for-each (lambda (script)
(let ((exe (string-append bin "/" script)))
(chmod exe #o555)
(wrap-script exe
#:guile #$(file-append guile-3.0 "/bin/guile")
`("PATH" ":" prefix ,path))))
(list "kaiju-convertMAR.py"
"kaiju-gbk2faa.pl"
"kaiju-makedb")))))))))
(inputs
(list perl zlib))
(list bzip2
coreutils
curl
gawk
guile-3.0 ;for wrap-script
gzip
perl
python-wrapper
tar
wget
zlib))
(home-page "http://kaiju.binf.ku.dk/")
(synopsis "Fast and sensitive taxonomic classification for metagenomics")
(description "Kaiju is a program for sensitive taxonomic classification