diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 70 |
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") |