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gnu: edirect: Update to 10.2.20181018.

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* gnu/packages/bioinformatics.scm (edirect): Update to 10.2.20181018.
[arguments]: Add simple check phase; simplify other phases.
[inputs]: Add perl-xml-simple.
This commit is contained in:
Ricardo Wurmus 2018-10-21 21:11:37 +02:00
parent 949fa34b84
commit c96ca68f31
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1 changed files with 26 additions and 20 deletions
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gnu/packages/bioinformatics.scm
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@ -2335,36 +2335,41 @@ quantitative phenotypes.")
(define-public edirect (define-public edirect
(package (package
(name "edirect") (name "edirect")
(version "4.10") (version "10.2.20181018")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/" (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect"
"versions/2016-05-03/edirect.tar.gz")) "/versions/" version
"/edirect-" version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli")))) "091f4aigzpbqih6h82nq566gkp3y07i72yqndmqskfgar1vwgci7"))))
(build-system perl-build-system) (build-system perl-build-system)
(arguments (arguments
`(#:tests? #f ;no "check" target `(#:phases
#:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(delete 'configure) (delete 'configure)
(delete 'build) (delete 'build)
(delete 'check) ; simple check after install
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let ((target (string-append (assoc-ref outputs "out") (install-file "edirect.pl"
"/bin"))) (string-append (assoc-ref outputs "out") "/bin"))
(mkdir-p target) #t))
(install-file "edirect.pl" target) (add-after 'install 'wrap-program
#t))) (lambda* (#:key outputs #:allow-other-keys)
(add-after
'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Make sure 'edirect.pl' finds all perl inputs at runtime. ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
(let* ((out (assoc-ref outputs "out")) (let* ((out (assoc-ref outputs "out"))
(path (getenv "PERL5LIB"))) (path (getenv "PERL5LIB")))
(wrap-program (string-append out "/bin/edirect.pl") (wrap-program (string-append out "/bin/edirect.pl")
`("PERL5LIB" ":" prefix (,path))))))))) `("PERL5LIB" ":" prefix (,path))))
#t))
(add-after 'wrap-program 'check
(lambda* (#:key outputs #:allow-other-keys)
(invoke (string-append (assoc-ref outputs "out")
"/bin/edirect.pl")
"-filter" "-help")
#t)))))
(inputs (inputs
`(("perl-html-parser" ,perl-html-parser) `(("perl-html-parser" ,perl-html-parser)
("perl-encode-locale" ,perl-encode-locale) ("perl-encode-locale" ,perl-encode-locale)
@ -2380,6 +2385,7 @@ quantitative phenotypes.")
("perl-net-http" ,perl-net-http) ("perl-net-http" ,perl-net-http)
("perl-uri" ,perl-uri) ("perl-uri" ,perl-uri)
("perl-www-robotrules" ,perl-www-robotrules) ("perl-www-robotrules" ,perl-www-robotrules)
("perl-xml-simple" ,perl-xml-simple)
("perl" ,perl))) ("perl" ,perl)))
(home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/") (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/")
(synopsis "Tools for accessing the NCBI's set of databases") (synopsis "Tools for accessing the NCBI's set of databases")