ryan77627/guix
1
0
Fork 0
mirror of https://git.in.rschanz.org/ryan77627/guix.git synced 2025-01-13 22:50:23 -05:00
Code Issues Projects Releases Packages Wiki Activity Actions

gnu: kaiju: Update to 1.9.0.

Browse source 
* 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
No known key found for this signature in database
GPG key ID: 197A5888235FACAC
1 changed files with 37 additions and 16 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

43
gnu/packages/bioinformatics.scm
View file

@ -4845,7 +4845,7 @@ (define-public khmer
(define-public kaiju (define-public kaiju
(package (package
(name "kaiju") (name "kaiju")
(version "1.6.3") (version "1.9.0")
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
@ -4854,24 +4854,45 @@ (define-public kaiju
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"119pzi0ddzv9mjg4wwa6han0cwr3k3ssn7kirvsjfcq05mi5ka0x")))) "1hfmadkfs6jjd7l3byly5xxb0ifm3dm1wis11sjbqfcv6l89snmg"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ; There are no tests. (list
#:tests? #f ; There are no tests.
#:phases #:phases
(modify-phases %standard-phases #~(modify-phases %standard-phases
(delete 'configure) (delete 'configure)
(add-before 'build 'move-to-src-dir (add-before 'build 'move-to-src-dir
(lambda _ (chdir "src") #t)) (lambda _ (chdir "src")))
(replace 'install (replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys) (lambda _
(let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (let ((bin (string-append #$output "/bin")))
(mkdir-p bin) (mkdir-p bin)
(chdir "..") (copy-recursively "../bin" bin)
(copy-recursively "bin" bin)) (let ((path (search-path-as-list '("bin")
#t))))) '#$(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 (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/") (home-page "http://kaiju.binf.ku.dk/")
(synopsis "Fast and sensitive taxonomic classification for metagenomics") (synopsis "Fast and sensitive taxonomic classification for metagenomics")
(description "Kaiju is a program for sensitive taxonomic classification (description "Kaiju is a program for sensitive taxonomic classification