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-rw-r--r--gnu/packages/bioinformatics.scm70
1 files changed, 70 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c076736da4..2355cbf9cf 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 National Center
+for Biotechnology Information's (NCBI) set of interconnected
+databases (publication, sequence, structure, gene, variation, expression,
+etc.) from a terminal. 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")