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22/28: gnu: edirect: Update to 10.2.20181018.
From: |
Ricardo Wurmus |
Subject: |
22/28: gnu: edirect: Update to 10.2.20181018. |
Date: |
Sun, 21 Oct 2018 17:07:01 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit c96ca68f31619ed678720fc1dc6bbf0906ce5638
Author: Ricardo Wurmus <address@hidden>
Date: Sun Oct 21 21:11:37 2018 +0200
gnu: edirect: Update to 10.2.20181018.
* gnu/packages/bioinformatics.scm (edirect): Update to 10.2.20181018.
[arguments]: Add simple check phase; simplify other phases.
[inputs]: Add perl-xml-simple.
---
gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++------------------
1 file changed, 26 insertions(+), 20 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d0f4429..a806fd5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2335,36 +2335,41 @@ quantitative phenotypes.")
(define-public edirect
(package
(name "edirect")
- (version "4.10")
+ (version "10.2.20181018")
(source (origin
(method url-fetch)
- (uri (string-append
"ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
- "versions/2016-05-03/edirect.tar.gz"))
+ (uri (string-append
"ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect"
+ "/versions/" version
+ "/edirect-" version ".tar.gz"))
(sha256
(base32
- "15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli"))))
+ "091f4aigzpbqih6h82nq566gkp3y07i72yqndmqskfgar1vwgci7"))))
(build-system perl-build-system)
(arguments
- `(#:tests? #f ;no "check" target
- #:phases
+ `(#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
+ (delete 'check) ; simple check after install
(replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((target (string-append (assoc-ref outputs "out")
- "/bin")))
- (mkdir-p target)
- (install-file "edirect.pl" target)
- #t)))
- (add-after
- 'install 'wrap-program
- (lambda* (#:key inputs outputs #:allow-other-keys)
- ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
- (let* ((out (assoc-ref outputs "out"))
- (path (getenv "PERL5LIB")))
- (wrap-program (string-append out "/bin/edirect.pl")
- `("PERL5LIB" ":" prefix (,path)))))))))
+ (lambda* (#:key outputs #:allow-other-keys)
+ (install-file "edirect.pl"
+ (string-append (assoc-ref outputs "out") "/bin"))
+ #t))
+ (add-after 'install 'wrap-program
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
+ (let* ((out (assoc-ref outputs "out"))
+ (path (getenv "PERL5LIB")))
+ (wrap-program (string-append out "/bin/edirect.pl")
+ `("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
`(("perl-html-parser" ,perl-html-parser)
("perl-encode-locale" ,perl-encode-locale)
@@ -2380,6 +2385,7 @@ quantitative phenotypes.")
("perl-net-http" ,perl-net-http)
("perl-uri" ,perl-uri)
("perl-www-robotrules" ,perl-www-robotrules)
+ ("perl-xml-simple" ,perl-xml-simple)
("perl" ,perl)))
(home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/")
(synopsis "Tools for accessing the NCBI's set of databases")
- branch master updated (f7618bf -> f8ee22f), Ricardo Wurmus, 2018/10/21
- 28/28: gnu: flexbar: Update to 3.4.0., Ricardo Wurmus, 2018/10/21
- 26/28: gnu: khmer: Update to 2.1.2., Ricardo Wurmus, 2018/10/21
- 22/28: gnu: edirect: Update to 10.2.20181018.,
Ricardo Wurmus <=
- 27/28: gnu: seqan: Update to 2.4.0., Ricardo Wurmus, 2018/10/21
- 24/28: gnu: fasttree: Use INVOKE., Ricardo Wurmus, 2018/10/21
- 23/28: gnu: express-beta-diversity: Update to 1.0.8., Ricardo Wurmus, 2018/10/21
- 20/28: gnu: discrover: Fetch from git., Ricardo Wurmus, 2018/10/21
- 17/28: gnu: Add texlive-latex-readarray., Ricardo Wurmus, 2018/10/21
- 18/28: gnu: Add texlive-latex-verbatimbox., Ricardo Wurmus, 2018/10/21
- 14/28: gnu: diamond: Fetch from git., Ricardo Wurmus, 2018/10/21
- 11/28: gnu: eolie: Update to 0.9.45., Ricardo Wurmus, 2018/10/21
- 25/28: gnu: python-screed: Update to 1.0., Ricardo Wurmus, 2018/10/21
- 19/28: gnu: Add texlive-latex-examplep., Ricardo Wurmus, 2018/10/21