diff options
author | Roel Janssen | 2016-03-15 16:58:59 +0100 |
---|---|---|
committer | Roel Janssen | 2016-03-15 16:58:59 +0100 |
commit | 904e605a2a881afe50ac5ae5950739d2fa0189c8 (patch) | |
tree | 068cef596458e187e5c03a1e3cb1306e29bceb6b /gn/packages/java.scm | |
parent | 95daf655ee7eb4647cb295b29335ac838b805cc0 (diff) | |
download | guix-bioinformatics-904e605a2a881afe50ac5ae5950739d2fa0189c8.tar.gz |
Added Java packages, working, WIP and ON HOLD.
Diffstat (limited to 'gn/packages/java.scm')
-rw-r--r-- | gn/packages/java.scm | 299 |
1 files changed, 299 insertions, 0 deletions
diff --git a/gn/packages/java.scm b/gn/packages/java.scm new file mode 100644 index 0000000..3fce390 --- /dev/null +++ b/gn/packages/java.scm @@ -0,0 +1,299 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2016 Roel Janssen <roel@gnu.org> +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. + +(define-module (gnu packages java) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix utils) + #:use-module (guix download) + #:use-module (guix git-download) + #:use-module (guix svn-download) + #:use-module (guix build-system gnu) + #:use-module (guix build-system ant) + #:use-module (gnu packages) + #:use-module (gnu packages autotools) + #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages compression) + #:use-module (gnu packages gcc) + #:use-module (gnu packages java) + #:use-module (gnu packages perl) + #:use-module (gnu packages certs) + #:use-module (gnu packages zip)) + +;; ---------------------------------------------------------------------------- +;; WORKING PACKAGES +;; ---------------------------------------------------------------------------- + +(define-public xz-java + (package + (name "xz-java") + (version "1.5") + (source (origin + (method url-fetch) + (uri (string-append "http://tukaani.org/xz/" + name "-" version ".zip")) + (sha256 + (base32 "0x6vn9dp9kxk83x2fp3394n95dk8fx9yg8jns9371iqsn0vy8ih1")))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; There's no test target. + #:jdk ,icedtea-7 + #:phases + (modify-phases %standard-phases + (replace 'unpack + (lambda _ + (mkdir-p "source") + (chdir "source") + (zero? (system* "unzip" (assoc-ref %build-inputs "source"))))) + (replace 'install + (lambda _ + (let ((out (string-append (assoc-ref %outputs "out") + "/share/java/xz/"))) + (mkdir-p out) + (copy-file "build/jar/xz.jar" (string-append out "/xz-1.5.jar")))))))) + (native-inputs + `(("unzip" ,unzip))) + (home-page "http://tukaani.org/xz/java.html") + (synopsis "Implementation of XZ data compression in pure Java") + (description "This aims to be a complete implementation of XZ data +compression in pure Java. Single-threaded streamed compression and +decompression and random access decompression have been fully implemented.") + (license license:public-domain))) + +(define-public jakarta-oro + (package + (name "jakarta-oro") + (version "2.0.8") + (source (origin + (method url-fetch) + (uri (string-append "http://archive.apache.org/dist/jakarta/oro/" + name "-" version ".tar.gz")) + (sha256 + (base32 "0rpmnsskiwmsy8r0sckz5n5dbvh3vkxx8hpm177c754r8xy3qksc")))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; There is no 'check' target + #:phases + (modify-phases %standard-phases + (replace 'install + (lambda _ + (let ((out (string-append (assoc-ref %outputs "out") + "/share/java/oro/"))) + (mkdir-p out) + (copy-file "jakarta-oro-2.0.8.jar" (string-append out "/oro-2.0.8.jar")))))) + )) + (home-page "http://jakarta.apache.org/oro/") + (synopsis "Set of text-processing Java classes") + (description "The Jakarta-ORO Java classes are a set of text-processing +Java classes that provide Perl5 compatible regular expressions, AWK-like regular +expressions, glob expressions, and utility classes for performing substitutions, +splits, filtering filenames, etc.") + (license license:asl1.1))) + +;; ---------------------------------------------------------------------------- +;; IN PROGRESS +;; ---------------------------------------------------------------------------- + +(define-public jsch + (package + (name "jsch") + (version "0.1.53") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge.net/jsch/" name "/" + version "/" name "-" version ".zip")) + (sha256 + (base32 "1729j7khwj6yvkr26fjaf273i3krhz2n1m3mbv5ms4x00qrhrxdn")))) + (build-system ant-build-system) + (home-page "http://www.jcraft.com/jsch/") + (synopsis "JSch is a pure Java implementation of SSH2") + (description "JSch is a pure Java implementation of SSH2. JSch allows you +to connect to an sshd server and use port forwarding, X11 forwarding, file +transfer, etc., and you can integrate its functionality into your own Java +programs.") + (license license:bsd-3))) + +(define-public commons-vfs + (package + (name "commons-vfs") + (version "2.0") + (source (origin + (method url-fetch) + (uri (string-append + "http://mirrors.supportex.net/apache/commons/vfs/source/" + name "-" version "-src.tar.gz")) + (sha256 + (base32 "1gkfg9g14kjkh2kf041ssdz9xnw7hpfmdsyrs1bbhyzikwg4s3d9")))) + (build-system ant-build-system) + (home-page "https://commons.apache.org/proper/commons-vfs/") + (synopsis "Commons Virtual File System API for Java") + (description "Commons VFS provides a single API for accessing various +different file systems. It presents a uniform view of the files from various +different sources, such as the files on local disk, on an HTTP server, or +inside a Zip archive. ") + (license license:asl2.0))) + +(define-public ivy +;; Ivy tries to download the following packages: +;; - https://repo1.maven.org/maven2/org/apache/ant/ant/1.7.1/ant-1.7.1.jar => We have ant-1.9.6 +;; - https://repo1.maven.org/maven2/org/apache/ant/ant-nodeps/1.7.1/ant-nodeps-1.7.1.jar => Probably not needed +;; - https://repo1.maven.org/maven2/org/apache/ant/ant-trax/1.7.1/ant-trax-1.7.1.jar => Classes moved to ant.jar +;; - https://repo1.maven.org/maven2/commons-httpclient/commons-httpclient/3.0/commons-httpclient-3.0.jar +;; - https://repo1.maven.org/maven2/oro/oro/2.0.8/oro-2.0.8.jar => Packaged +;; - https://repo1.maven.org/maven2/commons-vfs/commons-vfs/1.0/commons-vfs-1.0.jar +;; - https://repo1.maven.org/maven2/com/jcraft/jsch/0.1.50/jsch-0.1.50.jar +;; - https://repo1.maven.org/maven2/com/jcraft/jsch.agentproxy/0.0.6/jsch.agentproxy-0.0.6.jar +;; - https://repo1.maven.org/maven2/com/jcraft/jsch.agentproxy.connector-factory/0.0.6/jsch.agentproxy.connector-factory-0.0.6.jar +;; - https://repo1.maven.org/maven2/com/jcraft/jsch.agentproxy.jsch/0.0.6/jsch.agentproxy.jsch-0.0.6.jar +;; - https://repo1.maven.org/maven2/org/bouncycastle/bcpg-jdk14/1.45/bcpg-jdk14-1.45.jar +;; - https://repo1.maven.org/maven2/org/bouncycastle/bcprov-jdk14/1.45/bcprov-jdk14-1.45.jar +;; - https://repo1.maven.org/maven2/junit/junit/3.8.2/junit-3.8.2.jar +;; - https://repo1.maven.org/maven2/commons-lang/commons-lang/2.6/commons-lang-2.6.jar +;; - https://repo1.maven.org/maven2/org/apache/ant/ant-testutil/1.7.0/ant-testutil-1.7.0.jar +;; - https://repo1.maven.org/maven2/ant/ant-launcher/1.6.2/ant-launcher-1.6.2.jar +;; - https://repo1.maven.org/maven2/ant-contrib/ant-contrib/1.0b3/ant-contrib-1.0b3.jar +;; - https://repo1.maven.org/maven2/xerces/xercesImpl/2.6.2/xercesImpl-2.6.2.jar +;; - https://repo1.maven.org/maven2/xerces/xmlParserAPIs/2.6.2/xmlParserAPIs-2.6.2.jar + (package + (name "ivy") + (version "2.4.0") + (source (origin + (method url-fetch) + (uri (string-append "http://ftp.nluug.nl/internet/apache/ant/" name "/" + version "/apache-" name "-" version "-src.tar.gz")) + (sha256 + (base32 "1xkfn57g2m7l6y0xdq75x5rnrgk52m9jx2xah70g3ggl8750hbr0")))) + (build-system ant-build-system) + (inputs + `(("nss-certs" ,nss-certs))) + (home-page "http://ant.apache.org/ivy/") + (synopsis "Dependency manager for Ant") + (description "Apache Ivy is a popular dependency manager focusing on +flexibility and simplicity.") + (license license:asl2.0))) + + +;; ---------------------------------------------------------------------------- +;; ON HOLD: WAITING FOR MAVEN PACKAGES +;; ---------------------------------------------------------------------------- + +;; TODO: Needs commons-compress +;; (define-public ant-compress +;; (package +;; (name "ant-compress") +;; (version "1.4") +;; (source (origin +;; (method url-fetch) +;; (uri "https://www.apache.org/dist/ant/antlibs/compress/source/apache-ant-compress-1.4-src.tar.gz")) +;; (sha256 +;; (base32 "17v5i11srmi12ckgrvhlwn0gvapgizs5672x252h143r0ya4c04d"))) +;; )) + +;; TODO: Needs Maven. +;; (define-public commons-compress +;; (package +;; (name "apache-commons-compress") +;; (version "1.10") +;; (source (origin +;; (method url-fetch) +;; (uri ("http://ftp.tudelft.nl/apache//commons/compress/source/commons-compress-1.10-src.tar.gz"))) +;; (sha256 +;; (base32 "06b40k9dmgqkga3qmfpgzq87jf3fkcxnwaiyczclh58yibg19604"))) +;; )) + +;; TODO: Needs Maven. +;; (define-public jcommander +;; (package +;; (name "jcommander") +;; (version "1.48") +;; (source (origin +;; (method url-fetch) +;; (uri (string-append "https://github.com/cbeust/jcommander/archive/" +;; name "-" version ".tar.gz")) +;; (sha256 +;; (base32 "1qn56hd6sxkfdv9j6pwf8c7ia00n39zry236a6achc87wq2kmfnw")))) +;; (build-system ant-build-system) +;; (home-page "http://jcommander.org/") +;; (synopsis "Java framework for parsing command line parameters") +;; (description "JCommander is a very small Java framework that makes it +;; trivial to parse command line parameters. ") +;; (license license:asl2.0))) + +;; TODO: Needs Maven. +;; (define-public maven-remote-resources-plugin +;; (package +;; (name "maven-remote-resources-plugin") +;; (version "1.5") +;; (source (origin +;; (method svn-fetch) +;; (uri (svn-reference +;; (url (string-append "http://svn.apache.org/viewvc/maven/plugins/tags/" +;; name "-" version)) +;; (revision 1513840))) +;; (file-name (string-append name "-" version "-checkout")) +;; (sha256 +;; (base32 "1g0iavyb34kvs3jfrx2hfnr8lr11m39sj852cy7528wva1glfl4i")))) +;; (build-system ant-build-system) +;; (home-page "https://maven.apache.org/plugins/maven-remote-resources-plugin/") +;; (synopsis "") +;; (description "") +;; (license license:asl2.0))) + +;; TODO: Needs Maven. +;; (define-public junit +;; (package +;; (name "junit") +;; (version "4.12") +;; (source (origin +;; (method url-fetch) +;; (uri (string-append "https://github.com/junit-team/" +;; name "/archive/r" version ".tar.gz")) +;; (sha256 +;; (base32 "1r6ww2y3jpbpqh03r0966xxiz2vs8n72g6n6l0sjs3aspy56v8b1")))) +;; (build-system ant-build-system) +;; (home-page "http://junit.org/") +;; (synopsis "Framework to write repeatable tests") +;; (description "JUnit is a simple framework to write repeatable tests. It is +;; an instance of the xUnit architecture for unit testing frameworks.") +;; (license license:asl2.0))) + +(define-public maven + (package + (name "maven") + (version "3.3.9") + (source (origin + (method url-fetch) + (uri (string-append "http://apache.proserve.nl/maven/maven-3/" + version "/source/apache-maven-" version "-src.tar.gz")) + (sha256 + (base32 "1g0iavyb34kvs3jfrx2hfnr8lr11m39sj852cy7528wva1glfl4i")))) + (build-system ant-build-system) + (arguments + `(#:make-flags "-Dmaven.home=build/" + #:phases + (modify-phases %standard-phases + (add-before 'build 'set-m2-variable + (lambda _ + (setenv "M2_HOME" (string-append (assoc-ref %outputs "out") "/maven-3.3.9"))))))) + (home-page "https://maven.apache.org/") + (synopsis "") + (description "Apache Maven is a software project management and +comprehension tool. Based on the concept of a project object model (POM), +Maven can manage a project's build, reporting and documentation from a central +piece of information.") + (license license:asl2.0))) |