[gentoo-commits] proj/sci:master commit in: sci-biology/NGSEPplugin-bin/, sci-biology/NGSEPplugin/, ...

[Martin Mokrejs]

commit:     225240b5c35e442b575dd91b659c1b8171a88397
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Fri Jan 10 16:01:02 2020 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 10 16:06:00 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=225240b5

sci-biology/NGSEPcore-bin: binaries from upstream
sci-biology/NGSEPplugin-bin: upstream binaries
sci-biology/NGSEPplugin: add current HOMEPAGE

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 .../NGSEPcore-bin/NGSEPcore-bin-3.3.1.ebuild       | 37 ++++++++++++++++++++++
 sci-biology/NGSEPcore-bin/metadata.xml             | 15 +++++++++
 .../NGSEPplugin-bin/NGSEPplugin-bin-3.3.1.ebuild   | 28 ++++++++++++++++
 sci-biology/NGSEPplugin-bin/metadata.xml           | 15 +++++++++
 sci-biology/NGSEPplugin/NGSEPplugin-3.3.1.ebuild   |  5 +--
 5 files changed, 98 insertions(+), 2 deletions(-)

diff --git a/sci-biology/NGSEPcore-bin/NGSEPcore-bin-3.3.1.ebuild b/sci-biology/NGSEPcore-bin/NGSEPcore-bin-3.3.1.ebuild
new file mode 100644
index 000000000..8758da3ac
--- /dev/null
+++ b/sci-biology/NGSEPcore-bin/NGSEPcore-bin-3.3.1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2020 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/Library/NGSEPcore_3.3.1.jar
+	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 -> ${P}_QuickStart.txt"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+	dev-java/htsjdk"
+#	dev-java/jsci-bin
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"
+
+src_unpack(){
+	echo
+}
+
+src_install(){
+	java-pkg_dojar "${DISTDIR}"/*.jar
+	dodoc "${DISTDIR}"/${P}_UserManual.pdf \
+		"${DISTDIR}"/${P}_Tutorial.txt \
+		"${DISTDIR}"/${P}_QuickStart.txt
+}

diff --git a/sci-biology/NGSEPcore-bin/metadata.xml b/sci-biology/NGSEPcore-bin/metadata.xml
new file mode 100644
index 000000000..642261079
--- /dev/null
+++ b/sci-biology/NGSEPcore-bin/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>mmokrejs@×××××××××××××××.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@g.o</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="sourceforge">ngsep</remote-id>
+	</upstream>
+</pkgmetadata>

diff --git a/sci-biology/NGSEPplugin-bin/NGSEPplugin-bin-3.3.1.ebuild b/sci-biology/NGSEPplugin-bin/NGSEPplugin-bin-3.3.1.ebuild
new file mode 100644
index 000000000..f2a452138
--- /dev/null
+++ b/sci-biology/NGSEPplugin-bin/NGSEPplugin-bin-3.3.1.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="NGSEP with Eclipse Plugin (CNV and indel discovery)"
+HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home
+	https://github.com/NGSEP/NGSEPplugin"
+SRC_URI="https://sourceforge.net/projects/ngsep/files/OnlyPlugin/NGSEPplugin_3.3.1.201903140636.jar"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+	>=virtual/jdk-1.7:*
+	sci-biology/NGSEPcore-bin"
+RDEPEND="${DEPEND}
+	>=virtual/jre-1.7:*"
+
+S="${WORKDIR}"
+
+src_install(){
+	java-pkg_dojar "${DISTDIR}"/*.jar
+}

diff --git a/sci-biology/NGSEPplugin-bin/metadata.xml b/sci-biology/NGSEPplugin-bin/metadata.xml
new file mode 100644
index 000000000..642261079
--- /dev/null
+++ b/sci-biology/NGSEPplugin-bin/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>mmokrejs@×××××××××××××××.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@g.o</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="sourceforge">ngsep</remote-id>
+	</upstream>
+</pkgmetadata>

diff --git a/sci-biology/NGSEPplugin/NGSEPplugin-3.3.1.ebuild b/sci-biology/NGSEPplugin/NGSEPplugin-3.3.1.ebuild
index ec13ffa46..736121efb 100644
--- a/sci-biology/NGSEPplugin/NGSEPplugin-3.3.1.ebuild
+++ b/sci-biology/NGSEPplugin/NGSEPplugin-3.3.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -6,7 +6,8 @@ EAPI=7
 inherit java-pkg-2 java-ant-2
 
 DESCRIPTION="NGSEP with Eclipse Plugin (CNV and indel discovery)"
-HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home"
+HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home
+	https://github.com/NGSEP/NGSEPplugin"
 SRC_URI="https://sourceforge.net/projects/ngsep/files/SourceCode/NGSEPplugin_${PV}.tar.gz"
 
 LICENSE="GPL-3"