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