diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2022-10-04 23:07:19 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2022-10-04 23:10:56 +0200 |
| commit | 9ed65e6af77893b658a7159b091b5002892c2f95 (patch) | |
| tree | 2f2228b37bc8cd3eef59fa2ac696b85b2d497845 | |
| parent | a96ebe47b0686b5dd7ebe5fc133073abce559f4d (diff) | |
gnu: kaiju: Update to 1.9.0.
* 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.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 53 |
1 files changed, 37 insertions, 16 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 249b956c88..0404253193 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4845,7 +4845,7 @@ data.") (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 @@ data.") (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 |