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gnu: krona-tools: Install download scripts.

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* gnu/packages/web.scm (krona-tools)[inputs]: Add curl and make.
[arguments]: Patch and install update scripts to /share.
This commit is contained in:
Ricardo Wurmus 2021-04-28 10:15:43 +02:00
parent fe28f395bc
commit ffd5bc9600
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GPG key ID: 197A5888235FACAC
1 changed files with 33 additions and 4 deletions
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37
gnu/packages/web.scm
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@ -1198,11 +1198,13 @@ (define-public krona-tools
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin"))
(perl (string-append (assoc-ref outputs "out")
"/lib/perl5/site_perl/krona-tools/lib")))
"/lib/perl5/site_perl/krona-tools/lib"))
(share (string-append (assoc-ref outputs "out")
"/share/krona-tools")))
(mkdir-p bin)
(for-each
(lambda (script)
(let* ((executable (string-append "scripts/" script ".pl")))
(let ((executable (string-append "scripts/" script ".pl")))
;; Prefix executables with 'kt' as install script does.
(copy-file executable (string-append bin "/kt" script))))
'("ClassifyBLAST"
@ -1230,7 +1232,32 @@ (define-public krona-tools
(copy-recursively directory
(string-append perl "/../" directory)))
(list "data" "img" "taxonomy" "src"))
(install-file "lib/KronaTools.pm" perl))))
(install-file "lib/KronaTools.pm" perl)
;; Install downloaders
(substitute* "updateAccessions.sh"
(("ktPath=.*") (string-append "ktPath=" share "\n")))
(substitute* "updateTaxonomy.sh"
(("ktPath=.*") (string-append "ktPath=" share "\n"))
(("command -v curl")
(string-append "command -v " (which "curl")))
(("curl -s")
(string-append (which "curl") " -s"))
(("curl\\$timestring")
(string-append (which "curl") "$timestring"))
(("perl -M")
(string-append (which "perl") " -M"))
(("make ")
(string-append (which "make") " ")))
(for-each (lambda (file)
(install-file file (string-append share "/scripts")))
'("scripts/extractTaxonomy.pl"
"scripts/accession2taxid.make"
"scripts/taxonomy.make"))
(for-each (lambda (file)
(install-file file share))
'("updateAccessions.sh"
"updateTaxonomy.sh")))))
(add-after 'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@ -1248,7 +1275,9 @@ (define-public krona-tools
(invoke (string-append (assoc-ref outputs "out") "/bin/ktImportText")
"ec.tsv")))))))
(inputs
`(("perl" ,perl)))
`(("curl" ,curl)
("make" ,gnu-make)
("perl" ,perl)))
(home-page "https://github.com/marbl/Krona/wiki")
(synopsis "Hierarchical data exploration with zoomable HTML5 pie charts")
(description