commit: 26f7eab8fcc5e6148f85e81a876d1362c28c8e4f Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Mar 27 16:23:05 2019 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Mar 27 16:23:05 2019 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=26f7eab8
sci-biology/NGSEPcore: some improvements with the package Still unfinished work. Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz> sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild | 37 ++++++++++++++++++++++++++++ sci-biology/NGSEPcore/metadata.xml | 15 +++++++++++ 2 files changed, 52 insertions(+) diff --git a/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild new file mode 100644 index 000000000..3f844bf16 --- /dev/null +++ b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="NGSEP (CNV and indel discovery)" +HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home"; +SRC_URI="https://sourceforge.net/projects/ngsep/files/SourceCode/NGSEPcore_${PV}.tar.gz + https://sourceforge.net/projects/ngsep/files/training/UserManualNGSEP_V330.pdf -> ${P}_UserManual.pdf + https://sourceforge.net/projects/ngsep/files/training/Tutorial.txt -> ${P}_Tutorial.txt + https://sourceforge.net/projects/ngsep/files/training/QuickStart.txt -> ${P}_QuickStart.txt" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="dev-java/htsjdk" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${PN}_${PV}" + +src_prepare(){ + rm -f *.jar lib/htsjdk-1.129.jar || die + default +} + +src_compile(){ + make -j1 +} + +src_install(){ + java-pkg_dojar *.jar + dodoc "$DISTDIR}"/${P}_user_manual.pdf +} diff --git a/sci-biology/NGSEPcore/metadata.xml b/sci-biology/NGSEPcore/metadata.xml new file mode 100644 index 000000000..642261079 --- /dev/null +++ b/sci-biology/NGSEPcore/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">ngsep</remote-id> + </upstream> +</pkgmetadata>
