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gnu: krona-tools: Update to 2.7.

* gnu/packages/web.scm (krona-tools): Update to 2.7.
[arguments]: Delete 'build' phase.  Install new scripts.
version-0.11.0
Ben Woodcroft 6 years ago
parent
commit
9712ef8d42
No known key found for this signature in database GPG Key ID: E44DCCD146E0CCF4
  1. 32
      gnu/packages/web.scm

32
gnu/packages/web.scm

@ -283,7 +283,7 @@ parse JSON formatted strings back into the C representation of JSON objects.")
(define-public krona-tools
(package
(name "krona-tools")
(version "2.6.1")
(version "2.7")
(source (origin
(method url-fetch)
(uri (string-append
@ -291,24 +291,14 @@ parse JSON formatted strings back into the C representation of JSON objects.")
version "/KronaTools-" version ".tar"))
(sha256
(base32
"1fj5mf6wbwz7v74n2safbw7fpw32fik19vf0wdbc2srn82i8fiwz"))))
"0wvgllcqscsfb4xc09y3fqhx8i38pmr4w55vjs5y79wx56n710iq"))))
(build-system perl-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
;; There is no configure or build steps.
(delete 'configure)
(replace 'build
;; Remove 'use lib' statements from scripts as PERL5LIB is set
;; correctly during installation.
(lambda _
(for-each
(lambda (executable)
(display executable)(display "\n")
(substitute* executable
(("use lib \\(`ktGetLibPath`\\);") "")))
(find-files "scripts/" ".*"))
#t))
(delete 'build)
;; Install script "install.pl" expects the build directory to remain
;; after installation, creating symlinks etc., so re-implement it
;; here.
@ -325,7 +315,9 @@ parse JSON formatted strings back into the C representation of JSON objects.")
(copy-file executable (string-append bin "/kt" script))))
'("ClassifyBLAST"
"GetContigMagnitudes"
"GetTaxIDFromGI"
"GetLCA"
"GetTaxIDFromAcc"
"GetTaxInfo"
"ImportBLAST"
"ImportDiskUsage"
"ImportEC"
@ -341,13 +333,11 @@ parse JSON formatted strings back into the C representation of JSON objects.")
"ImportTaxonomy"
"ImportText"
"ImportXML"))
(copy-recursively "data" (string-append perl "/../data"))
(copy-recursively "img" (string-append perl "/../img"))
(copy-recursively "taxonomy" (string-append perl "/../taxonomy"))
(install-file "src/krona-2.0.js" (string-append perl "/../src"))
(substitute* "lib/KronaTools.pm"
(("`ktGetLibPath`")
(string-append "\"" perl "\"")))
(for-each
(lambda (directory)
(copy-recursively directory
(string-append perl "/../" directory)))
(list "data" "img" "taxonomy" "src"))
(install-file "lib/KronaTools.pm" perl))))
(add-after 'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)

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