diff options
-rw-r--r-- | sci-biology/jalview/ChangeLog | 7 | ||||
-rw-r--r-- | sci-biology/jalview/Manifest | 4 | ||||
-rw-r--r-- | sci-biology/jalview/jalview-2.4.ebuild | 60 | ||||
-rw-r--r-- | sci-biology/jalview/metadata.xml | 9 |
4 files changed, 80 insertions, 0 deletions
diff --git a/sci-biology/jalview/ChangeLog b/sci-biology/jalview/ChangeLog new file mode 100644 index 000000000..d83140491 --- /dev/null +++ b/sci-biology/jalview/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/jalview +# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 10 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: + New package, ebuild written by me + diff --git a/sci-biology/jalview/Manifest b/sci-biology/jalview/Manifest new file mode 100644 index 000000000..766297820 --- /dev/null +++ b/sci-biology/jalview/Manifest @@ -0,0 +1,4 @@ +DIST jalview_2_4.tar.gz 11319073 RMD160 770f57a9c9b7822c0b13d0dfa46977b95ad8384a SHA1 f0f69b3b4716285aece7fc914df3a3133baf1abe SHA256 c4fe3a4b214ed7f06d48bd88fd53e068c2151390ec8004acd6705bea47b4918a +EBUILD jalview-2.4.ebuild 1764 RMD160 02ce95fe3152ab424609b3789e60669e23d62d5c SHA1 da36d1747192093277de48e8a85c84991c58ff6e SHA256 79b2fa96a1a1f0109393e7f54b2ada9d506084d5b4436a5a22af3f3e44a82c29 +MISC ChangeLog 218 RMD160 691cb6907bf3038353f64854d9842ba4bdab3682 SHA1 9db1dfeee42326b0ea72b26101a2ed764fe2d382 SHA256 ee59ea378bf4fa6067d3d594c433d1e7f7475d37b8f07fb4916b032b8c346457 +MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 diff --git a/sci-biology/jalview/jalview-2.4.ebuild b/sci-biology/jalview/jalview-2.4.ebuild new file mode 100644 index 000000000..d1c1dea85 --- /dev/null +++ b/sci-biology/jalview/jalview-2.4.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/beast-mcmc/beast-mcmc-1.5.1.ebuild,v 1.1 2009/10/02 21:47:11 weaver Exp $ + +EAPI="2" + +EANT_GENTOO_CLASSPATH="jmol,castor-1.0,log4j,commons-logging,commons-discovery,wsdl4j,xerces-2,saaj,vecmath,javahelp,sun-jaf" +JAVA_ANT_REWRITE_CLASSPATH="true" +EANT_BUILD_TARGET="distclean makedist" +JAVA_PKG_IUSE="source doc" + +inherit java-pkg-2 java-ant-2 eutils + +DESCRIPTION="A multiple DNA sequence alignment editor" +HOMEPAGE="http://www.jalview.org/" +SRC_URI="http://www.jalview.org/source/jalview_2_4.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +COMMON_DEPS=">=sci-chemistry/jmol-11.0.2 <sci-chemistry/jmol-11.1 + dev-java/castor:1.0 + dev-java/log4j" +DEPEND=">=virtual/jdk-1.5 + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.5 + dev-java/commons-discovery + dev-java/commons-logging + dev-java/saaj + dev-java/xerces + dev-java/wsdl4j + dev-java/vecmath + dev-java/javahelp + dev-java/sun-jaf + dev-java/sun-javamail + ${COMMON_DEPS}" + +S="${WORKDIR}/${PN}" + +java_prepare() { + perl -i -ne'print unless /<jalopy/../<\/jalopy>/ or /<taskdef.+name="jalopy"/../<\/taskdef>/ or /<include name="jalview-jalopy.xml"/' build.xml + find -name '*.jar' | egrep -v '(vamsas|axis|jaxrpc|roxes-ant-tasks|regex|xml-apis)' | xargs rm -v +} + +src_install() { + java-pkg_dojar dist/*.jar + + MY_CP="" + for i in $(cd dist; ls *.jar); do + MY_CP="${MY_CP}:${ROOT}usr/share/${PN}/lib/$i" + done + java-pkg_dolauncher jalview --main jalview.bin.Jalview \ + --java_args "-cp ${MY_CP}:$(java-config -p ${EANT_GENTOO_CLASSPATH})" + + use source && java-pkg_dosrc src +# use doc && java-pkg_dojavadoc something - no docs to be seen + dodoc README doc/* +} diff --git a/sci-biology/jalview/metadata.xml b/sci-biology/jalview/metadata.xml new file mode 100644 index 000000000..3302123e5 --- /dev/null +++ b/sci-biology/jalview/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>weaver@gentoo.org</email> + <name>Andrey Kislyuk</name> + </maintainer> + <herd>sci-biology</herd> +</pkgmetadata> |