commit: 078f19efedf1e0abfa70e43de79bb284aa6578dc Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Mar 23 21:42:40 2014 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Mar 23 21:42:40 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=078f19ef
sci-biology/cgview-bin: new package, needs java team testing, maybe dev-java/batik is misisng svg USE flag? Package-Manager: portage-2.2.7 --- sci-biology/cgview-bin/ChangeLog | 10 ++++++ sci-biology/cgview-bin/cgview-bin-20131130.ebuild | 44 +++++++++++++++++++++++ sci-biology/cgview-bin/metadata.xml | 9 +++++ 3 files changed, 63 insertions(+) diff --git a/sci-biology/cgview-bin/ChangeLog b/sci-biology/cgview-bin/ChangeLog new file mode 100644 index 0000000..d8d6b14 --- /dev/null +++ b/sci-biology/cgview-bin/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/cgview-bin +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*cgview-bin-20131130 (23 Mar 2014) + + 23 Mar 2014; Martin Mokrejs <[email protected]> + +cgview-bin-20131130.ebuild, +metadata.xml: + sci-biology/cgview-bin: new package, needs java team testing, maybe dev- + java/batik is misisng svg USE flag? diff --git a/sci-biology/cgview-bin/cgview-bin-20131130.ebuild b/sci-biology/cgview-bin/cgview-bin-20131130.ebuild new file mode 100644 index 0000000..be563a9 --- /dev/null +++ b/sci-biology/cgview-bin/cgview-bin-20131130.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 + +# download 134MB in size! +DESCRIPTION="CGView Comparison Tool to compare genome sequences graphically (aka CCT)" +HOMEPAGE="http://stothard.afns.ualberta.ca/downloads/CCT"; +SRC_URI="http://www.ualberta.ca/~stothard/downloads/cgview_comparison_tool.zip"; + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND=">=dev-lang/perl-5.8.8 + >=sci-biology/ncbi-tools-2.2.15 + >=virtual/jre-1.4.2 + dev-java/xerces + dev-java/batik + dev-java/commons-lang + >=media-gfx/imagemagick-6 + >=sci-biology/bioperl-1.4.0" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/cgview_comparison_tool + +src_install() { + echo 'CCT_HOME='${EPREFIX}'/usr/share/cgview_comparison_tool' > "${S}/99cgview" + echo 'PATH="$PATH":"'${CCT_HOME}'/scripts"' >> "${S}/99cgview" + doenvd "${S}/99cgview" || die + #export PATH="$PATH":"${CCT_HOME}/scripts":/path/to/blast-2.2.25/bin + #export PERL5LIB="${CCT_HOME}"/lib/bioperl-1.2.3:"${CCT_HOME}"/lib/perl_modules:"$PERL5LIB" + + dobin bin/cgview.jar +} + +src_test(){ + ./update_cogs.sh || die + ./test.sh || die +} diff --git a/sci-biology/cgview-bin/metadata.xml b/sci-biology/cgview-bin/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/cgview-bin/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata>
