diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/web.scm | 96 |
1 files changed, 96 insertions, 0 deletions
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 5df4765d3c..bd30da2533 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2016 Jelle Licht <jlicht@fsfe.org> ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 Rene Saavedra <rennes@openmailbox.org> +;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -56,6 +57,7 @@ #:use-module (gnu packages icu4c) #:use-module (gnu packages lua) #:use-module (gnu packages base) + #:use-module (gnu packages perl) #:use-module (gnu packages python) #:use-module (gnu packages pcre) #:use-module (gnu packages pkg-config) @@ -274,6 +276,100 @@ easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects.") (license l:x11))) +(define-public krona-tools + (package + (name "krona-tools") + (version "2.6.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/marbl/Krona/releases/download/v" + version "/KronaTools-" version ".tar")) + (sha256 + (base32 + "1fj5mf6wbwz7v74n2safbw7fpw32fik19vf0wdbc2srn82i8fiwz")))) + (build-system perl-build-system) + (arguments + `(#:tests? #f ; no tests + #:phases + (modify-phases %standard-phases + ;; There is no configure or build steps. + (delete 'configure) + (replace 'build + ;; Remove 'use lib' statements from scripts as PERL5LIB is set + ;; correctly during installation. + (lambda _ + (for-each + (lambda (executable) + (display executable)(display "\n") + (substitute* executable + (("use lib \\(`ktGetLibPath`\\);") ""))) + (find-files "scripts/" ".*")) + #t)) + ;; Install script "install.pl" expects the build directory to remain + ;; after installation, creating symlinks etc., so re-implement it + ;; here. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin")) + (perl (string-append (assoc-ref outputs "out") + "/lib/perl5/site_perl")) + (share (string-append + (assoc-ref outputs "out") "/share/krona-tools"))) + (mkdir-p bin) + (for-each + (lambda (script) + (let* ((executable (string-append "scripts/" script ".pl"))) + ;; Prefix executables with 'kt' as install script does. + (copy-file executable (string-append bin "/kt" script)))) + '("ClassifyBLAST" + "GetContigMagnitudes" + "GetTaxIDFromGI" + "ImportBLAST" + "ImportDiskUsage" + "ImportEC" + "ImportFCP" + "ImportGalaxy" + "ImportKrona" + "ImportMETAREP-BLAST" + "ImportMETAREP-EC" + "ImportMGRAST" + "ImportPhymmBL" + "ImportRDP" + "ImportRDPComparison" + "ImportTaxonomy" + "ImportText" + "ImportXML")) + (mkdir-p share) + (copy-recursively "data" (string-append share "/data")) + (copy-recursively "img" (string-append share "/img")) + (copy-recursively "taxonomy" (string-append share "/taxonomy")) + (substitute* '("lib/KronaTools.pm") + (("taxonomyDir = \".libPath/../taxonomy\"") + (string-append "taxonomyDir = \"" share "/taxonomy\""))) + (install-file "lib/KronaTools.pm" perl)))) + (add-after 'install 'wrap-program + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (path (getenv "PERL5LIB"))) + (for-each + (lambda (executable) + (wrap-program executable + `("PERL5LIB" ":" prefix + (,(string-append out "/lib/perl5/site_perl"))))) + (find-files (string-append out "/bin/") ".*")))))))) + (inputs + `(("perl" ,perl))) + (home-page "https://github.com/marbl/Krona/wiki") + (synopsis "Hierarchical data exploration with zoomable HTML5 pie charts") + (description + "Krona is a flexible tool for exploring the relative proportions of +hierarchical data, such as metagenomic classifications, using a radial, +space-filling display. It is implemented using HTML5 and JavaScript, allowing +charts to be explored locally or served over the Internet, requiring only a +current version of any major web browser.") + (license l:bsd-3))) + (define-public rapidjson (package (name "rapidjson") |