[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/beagle/

[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/beagle/

[Andrew Ammerlaan]

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"
+}