* [PATCH] Add edirect.
@ 2015-05-27 13:16 Ricardo Wurmus
2015-05-27 15:29 ` Ludovic Courtès
0 siblings, 1 reply; 2+ messages in thread
From: Ricardo Wurmus @ 2015-05-27 13:16 UTC (permalink / raw)
To: guix-devel
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Hi Guix,
attached is a patch for "Entrez Direct" a tool for accessing the vast
online databases of NCBI.
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From 1808a6000260418ce7a3433cb75e904b854fcc53 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 27 May 2015 15:14:19 +0200
Subject: [PATCH] gnu: Add edirect.
* gnu/packages/bioinformatics.scm (edirect): New variable.
---
gnu/packages/bioinformatics.scm | 70 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 70 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b359a8a..30de73e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -24,6 +24,7 @@
#:use-module (guix git-download)
#:use-module (guix build-system gnu)
#:use-module (guix build-system cmake)
+ #:use-module (guix build-system perl)
#:use-module (guix build-system python)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
@@ -45,6 +46,7 @@
#:use-module (gnu packages tbb)
#:use-module (gnu packages textutils)
#:use-module (gnu packages vim)
+ #:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (gnu packages zip))
@@ -542,6 +544,74 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
other types of unwanted sequence from high-throughput sequencing reads.")
(license license:expat)))
+(define-public edirect
+ (package
+ (name "edirect")
+ (version "2.50")
+ (source (origin
+ (method url-fetch)
+ ;; Note: older versions are not retained.
+ (uri "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.zip")
+ (sha256
+ (base32
+ "08afhz2ph66h8h381hl1mqyxkdi5nbvzsyj9gfw3jfbdijnpi4qj"))))
+ (build-system perl-build-system)
+ (arguments
+ `(#:tests? #f ;no "check" target
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'build)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((target (string-append (assoc-ref outputs "out")
+ "/bin")))
+ (mkdir-p target)
+ (copy-file "edirect.pl"
+ (string-append target "/edirect.pl"))
+ #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)))))))))
+ (inputs
+ `(("perl-html-parser" ,perl-html-parser)
+ ("perl-encode-locale" ,perl-encode-locale)
+ ("perl-file-listing" ,perl-file-listing)
+ ("perl-html-tagset" ,perl-html-tagset)
+ ("perl-html-tree" ,perl-html-tree)
+ ("perl-http-cookies" ,perl-http-cookies)
+ ("perl-http-date" ,perl-http-date)
+ ("perl-http-message" ,perl-http-message)
+ ("perl-http-negotiate" ,perl-http-negotiate)
+ ("perl-lwp-mediatypes" ,perl-lwp-mediatypes)
+ ("perl-lwp-protocol-https" ,perl-lwp-protocol-https)
+ ("perl-net-http" ,perl-net-http)
+ ("perl-uri" ,perl-uri)
+ ("perl-www-robotrules" ,perl-www-robotrules)
+ ("perl" ,perl)))
+ (native-inputs
+ `(("unzip" ,unzip)))
+ (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288")
+ (synopsis "Tools for accessing the NCBI's set of databases")
+ (description
+ "Entrez Direct (EDirect) is a method for accessing the NCBI's set of
+interconnected databases (publication, sequence, structure, gene, variation,
+expression, etc.) from a terminal window. Functions take search terms from
+command-line arguments. Individual operations are combined to build
+multi-step queries. Record retrieval and formatting normally complete the
+process.
+
+EDirect also provides an argument-driven function that simplifies the
+extraction of data from document summaries or other results that are returned
+in structured XML format. This can eliminate the need for writing custom
+software to answer ad hoc questions.")
+ (license license:public-domain)))
+
(define-public express
(package
(name "express")
--
2.1.0
^ permalink raw reply related [flat|nested] 2+ messages in thread
* Re: [PATCH] Add edirect.
2015-05-27 13:16 [PATCH] Add edirect Ricardo Wurmus
@ 2015-05-27 15:29 ` Ludovic Courtès
0 siblings, 0 replies; 2+ messages in thread
From: Ludovic Courtès @ 2015-05-27 15:29 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> From 1808a6000260418ce7a3433cb75e904b854fcc53 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Wed, 27 May 2015 15:14:19 +0200
> Subject: [PATCH] gnu: Add edirect.
>
> * gnu/packages/bioinformatics.scm (edirect): New variable.
[...]
> + (description
> + "Entrez Direct (EDirect) is a method for accessing the NCBI's set of
Could you expand “NCBI” on the first occurrence?
Otherwise LGTM, thanks!
Ludo’.
^ permalink raw reply [flat|nested] 2+ messages in thread
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2015-05-27 15:29 ` Ludovic Courtès
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