commit: 87260b125c1a2977523f2ebb99c364c7bcd8d86c Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Sun Jan 10 12:20:17 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Sun Jan 10 12:20:17 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=87260b12
sci-biology/NGSEPcore: add version 4.0.3 Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild | 44 ++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild b/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild new file mode 100644 index 000000000..7dc343127 --- /dev/null +++ b/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2021 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 + https://github.com/NGSEP/NGSEPcore"; +SRC_URI="https://sourceforge.net/projects/ngsep/files/SourceCode/NGSEPcore_${PV}.tar.gz + https://sourceforge.net/projects/ngsep/files/training/ManualNGSEP_v${PV}.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 -> ${P}_QuickStart.txt" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=">=virtual/jdk-1.8" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${PN}_${PV}" + +src_prepare(){ + # recent versions of htsjdk now use gradle, + # which is not supported by portage + #rm lib/htsjdk-2.22.jar || die + # TODO: package dev-java/jsci + #rm lib/jsci-core.jar || die + default +} + +src_compile(){ + emake -j1 +} + +src_install(){ + java-pkg_dojar *.jar lib/*.jar + dodoc "${DISTDIR}"/${P}_UserManual.pdf \ + "${DISTDIR}"/${P}_Tutorial.txt \ + "${DISTDIR}"/${P}_QuickStart.txt \ + README.txt +}
