commit: 58757ad4c94dc19558955d6588a5f4b6ba7e195d Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Tue Jan 19 15:05:45 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Tue Jan 19 15:06:01 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=58757ad4
sci-biology/beagle: version bump, fix fetch Package-Manager: Portage-3.0.13, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> profiles/package.mask | 1 - sci-biology/beagle/beagle-4.0.ebuild | 22 ---------------------- sci-biology/beagle/beagle-5.1.ebuild | 30 ++++++++++++++++++++++++++++++ 3 files changed, 30 insertions(+), 23 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 6f2346e7b..a92b72a94 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -42,4 +42,3 @@ sci-biology/aghermann sci-biology/argo-bin sci-biology/bambino sci-biology/BBmap -sci-biology/beagle diff --git a/sci-biology/beagle/beagle-4.0.ebuild b/sci-biology/beagle/beagle-4.0.ebuild deleted file mode 100644 index 61a9463c6..000000000 --- a/sci-biology/beagle/beagle-4.0.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit java-pkg-2 java-ant-2 - -DESCRIPTION="Genotype calling/phasing, imputation of ungenotyped markers" -HOMEPAGE="http://faculty.washington.edu/browning/beagle/beagle.html"; -SRC_URI="http://faculty.washington.edu/browning/beagle/beagle.r1399.src.zip - http://faculty.washington.edu/browning/beagle/beagle.03Mar15.pdf - http://faculty.washington.edu/browning/beagle/run.beagle.r1399.example -> ${PN}-example.sh - http://faculty.washington.edu/browning/beagle/release_notes -> ${PN}-release_notes.txt" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND=">=virtual/jdk-1.7:*" -RDEPEND="${DEPEND} - sci-biology/conform-gt" diff --git a/sci-biology/beagle/beagle-5.1.ebuild b/sci-biology/beagle/beagle-5.1.ebuild new file mode 100644 index 000000000..38b04921c --- /dev/null +++ b/sci-biology/beagle/beagle-5.1.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit java-pkg-2 + +DESCRIPTION="Genotype calling/phasing, imputation of ungenotyped markers" +HOMEPAGE="https://faculty.washington.edu/browning/beagle/beagle.html"; +SRC_URI=" + https://faculty.washington.edu/browning/beagle/beagle.18May20.d20.jar + https://faculty.washington.edu/browning/beagle/beagle_${PV}_08Nov19.pdf + https://faculty.washington.edu/browning/beagle/run.beagle.18May20.d20.example -> ${PN}-example.sh +" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND=">=virtual/jdk-1.8:*" +RDEPEND="${DEPEND} + sci-biology/conform-gt" + +S="${WORKDIR}" + +src_install() { + java-pkg_newjar "${DISTDIR}/beagle.18May20.d20.jar" "${PN}.jar" + dodoc "${DISTDIR}/beagle_${PV}_08Nov19.pdf" + dodoc "${DISTDIR}/${PN}-example.sh" +}
