pkgmove from dev-java/ to sci-biology/

Signed-off-by: Patrice Clement <monsieurp@gentoo.org>
Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0x93491BB8

5 files changed, 198 insertions, 0 deletions

diff --git a/sci-biology/biojava/ChangeLog b/sci-biology/biojava/ChangeLog
new file mode 100644
index 000000000000..8369f17f1275
--- /dev/null
+++ b/sci-biology/biojava/ChangeLog
@@ -0,0 +1,26 @@
+# ChangeLog for dev-java/biojava
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/biojava/ChangeLog,v 1.1 2015/08/05 14:02:36 monsieurp Exp $
+
+  24 May 2014; Pacho Ramos <pacho@gentoo.org> metadata.xml:
+  Cleanup due #199047
+
+  20 Mar 2010; Petteri Räty <betelgeuse@gentoo.org> biojava-1.7.ebuild:
+  Keyword ~x86.
+
+*biojava-1.7 (10 Jul 2009)
+
+  10 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> +biojava-1.7.ebuild:
+  Version bump
+
+  07 Feb 2009; weaver <weaver@gentoo.org> metadata.xml:
+  Assume ownership
+
+*biojava-1.6 (25 Jan 2009)
+
+  25 Jan 2009; weaver <weaver@gentoo.org> +metadata.xml,
+  +biojava-1.6.ebuild:
+  Import from Java overlay, thanks to serkan
+
+  22 Jan 2009; Alistair Bush <ali_bush@gentoo.org> ChangeLog:
+  Add ChangeLog for QA.
diff --git a/sci-biology/biojava/Manifest b/sci-biology/biojava/Manifest
new file mode 100644
index 000000000000..cb407dbae521
--- /dev/null
+++ b/sci-biology/biojava/Manifest
@@ -0,0 +1,20 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA256
+
+DIST biojava-1.6-all.jar 24571007 SHA256 2d10334fe6022d1b64219505ba4d2a32027ab7218d775878506d3e7c00f6ce7e SHA512 300bd6e02fe052c810c52cb2cc4255628bee704af187ad746b97e57941778dc3a1996b3917db021d74db8c716f94c90c94c5a5e2d4bc212c06259381045f3034 WHIRLPOOL e5a52aaa6e9a9d6780d5f55b6d164db07388e9c595296d4e4a11dc241aa0745fa726279d19a0c97d1966b0a14c06af2b9b588873ad522aeeff881534f0871f10
+DIST biojava-1.7-all.jar 28062592 SHA256 5c5e7fc66bc79a07494fb7d935164ec2aab50dc2effb7644f89bfa4fc907bb3f SHA512 867862b45f014bcd1afd37691e91b948ede05e96f84c7051953d32dad49908781235aad80301e22a15fa8b4145e80c78cf3935d6e581a2e60b56c9308f8adaa8 WHIRLPOOL 5669293ce362e82562454c5902d523e69f64d90e117e75b5de844e0ef5866d250507b86f78245ac82f19932ad9aa196ad17d96a3f703187a3ab2daf00893af9b
+EBUILD biojava-1.6.ebuild 2004 SHA256 a6c787e1463ac3c9a6a15efd6d9d9f7827ca3688b6527feef910bb3dedf9b29d SHA512 2bbf7273f3149be82c604c485144ff6ebc9ce4fd222bf356ebefa38429a4f93e3b84947548967a23ce0591dca87da17062bb658b493b8062018a122cf5d0b3b0 WHIRLPOOL 1d05f7f4aa6762de077e79793dbd0e83c4bb80690d3741ccbed790d88ccb99ce3917876acda2783b356c9cbe8118ce80a4bc6d97dc4483857488fabe0dd3fbee
+EBUILD biojava-1.7.ebuild 2026 SHA256 9d994995677a07e18323e72e6c19fb09b4068bd0c1370e28022a55faa9c3e4a2 SHA512 5ab157b9ba634d85033911defc65b48d857386027dd64b95528b0932370042d7238a183b8c5113f769ed3e7b3b6950b80201840e1489429659756d6395f1ac94 WHIRLPOOL 8156bc40fb8284899d8e4a23ade8b45601e7fcbc3246c721ddfeee13ec349489a866c4623ae8b6e9cb2e7dd8b060110a3cb8c0a4d4e63d16e86e6adfa62732ae
+MISC ChangeLog 815 SHA256 3b4032bcb9b0d9f27bcd843196e5332d5301f404cea4334d392b11652beb8bee SHA512 b43456bff1ad36187d2666416956f069fbc89529a0603bd84532d49103849413278546fbdba8ce2a9a31a972116bdb88051122687fdcbccaf86a05620384d449 WHIRLPOOL 3ce15f2a8aef814454615644d53dc479d7f7663b1012a2bbc10b68b7322b6c8b35c1375d6e88ca9381eeea67c918c6b89b8ab4a88ab89c9db70c4f77387d83bf
+MISC metadata.xml 184 SHA256 b1eba987253b6431655eb740d92c9317127741c254ccf58811333144072fed15 SHA512 810509270c115326274543d26ae73517c79690223fdc33cecd2ac55a5ad2a0bc5bf773f52f865bfd1e57caaf6e932f4622d6403b3248a4bb50a9d782c43cec3b WHIRLPOOL a2e20616a149551b2873be9eb84ce99ebad34323db12c2ced66731775e69d9ef7fbf952256019d6e573f420bb87b37dd8e147e29a479c0480fc349345caaf467
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diff --git a/sci-biology/biojava/biojava-1.6.ebuild b/sci-biology/biojava/biojava-1.6.ebuild
new file mode 100644
index 000000000000..1a1373eccde8
--- /dev/null
+++ b/sci-biology/biojava/biojava-1.6.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/biojava/biojava-1.6.ebuild,v 1.1 2015/08/05 14:02:36 monsieurp Exp $
+
+# TODO:
+# -Fix javadoc generation OutOfMemoryError
+# -Add launchers for 2 apps in biojava-apps.jar
+# -Decide on demo packaging. (Whether to install its jar as done or sources by examples USE flag)
+
+EAPI=2
+
+#JAVA_PKG_IUSE="doc source test"
+JAVA_PKG_IUSE="source test"
+
+inherit eutils java-pkg-2 java-ant-2
+
+DESCRIPTION="A Java framework for processing biological data"
+HOMEPAGE="http://biojava.org"
+SRC_URI="http://www.biojava.org/download/bj16/all/${P}-all.jar"
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+COMMON_DEPEND="dev-java/jgrapht:0
+	dev-java/commons-cli:1
+	dev-java/commons-dbcp:0
+	dev-java/commons-pool:0
+	dev-java/bytecode:0"
+
+RDEPEND=">=virtual/jre-1.5
+	${COMMON_DEPEND}"
+DEPEND=">=virtual/jdk-1.5
+	app-arch/unzip
+	${COMMON_DEPEND}
+	test?
+	(
+		dev-java/junit:4
+		dev-java/ant-junit4
+	)"
+
+S="${WORKDIR}/biojava-live_${PV}"
+
+JAVA_ANT_IGNORE_SYSTEM_CLASSES="true"
+
+src_prepare() {
+	einfo "Removing budled jars."
+	find . -name "*.jar" -print -delete
+	rm -r doc/*
+	java-pkg_jar-from jgrapht jgrapht.jar jgrapht-jdk1.5.jar
+	java-pkg_jar-from commons-cli-1
+	java-pkg_jar-from commons-dbcp commons-dbcp.jar commons-dbcp-1.1.jar
+	java-pkg_jar-from commons-pool commons-pool.jar commons-pool-1.1.jar
+	java-pkg_jar-from bytecode
+}
+
+src_compile() {
+	#ANT_OPTS="${ANT_OPTS} -Xmx512m"
+	eant package-biojava package-biojava package-demos package-apps #$(use_doc javadocs-all)
+}
+
+src_install() {
+	java-pkg_newjar ant-build/biojava.jar ${PN}.jar
+	java-pkg_newjar ant-build/apps.jar ${PN}-apps.jar
+	java-pkg_newjar ant-build/demos.jar ${PN}-demos.jar
+	#use doc && java-pkg_dojavadoc ant-build/doc/{biojava,apps,demos}
+	use source && java-pkg_dosrc {src,apps,demos}/org
+}
+
+src_test() {
+	java-pkg_jar-from junit-4 junit.jar junit-4.4.jar
+	ANT_TASKS="ant-junit4" eant runtests
+}
diff --git a/sci-biology/biojava/biojava-1.7.ebuild b/sci-biology/biojava/biojava-1.7.ebuild
new file mode 100644
index 000000000000..759af51894d5
--- /dev/null
+++ b/sci-biology/biojava/biojava-1.7.ebuild
@@ -0,0 +1,73 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/biojava/biojava-1.7.ebuild,v 1.1 2015/08/05 14:02:36 monsieurp Exp $
+
+# TODO:
+# -Fix javadoc generation OutOfMemoryError
+# -Add launchers for 2 apps in biojava-apps.jar
+# -Decide on demo packaging. (Whether to install its jar as done or sources by examples USE flag)
+
+EAPI=2
+
+#JAVA_PKG_IUSE="doc source test"
+JAVA_PKG_IUSE="source test"
+
+inherit eutils java-pkg-2 java-ant-2
+
+DESCRIPTION="A Java framework for processing biological data"
+HOMEPAGE="http://biojava.org"
+SRC_URI="http://www.biojava.org/download/bj17/all/${P}-all.jar"
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+COMMON_DEPEND="dev-java/jgrapht:0
+	dev-java/commons-cli:1
+	dev-java/commons-dbcp:0
+	dev-java/commons-pool:0
+	dev-java/commons-collections:0
+	dev-java/bytecode:0"
+
+RDEPEND=">=virtual/jre-1.5
+	${COMMON_DEPEND}"
+DEPEND=">=virtual/jdk-1.5
+	app-arch/unzip
+	${COMMON_DEPEND}
+	test?
+	(
+		dev-java/junit:4
+		dev-java/ant-junit4
+	)"
+
+S="${WORKDIR}/biojava-${PV}"
+
+JAVA_ANT_IGNORE_SYSTEM_CLASSES="true"
+
+src_prepare() {
+	einfo "Removing bundled jars..."
+	find . -name "*.jar" -print -delete
+	java-pkg_jar-from jgrapht jgrapht.jar jgrapht-jdk1.5.jar
+	java-pkg_jar-from commons-cli-1
+	java-pkg_jar-from commons-dbcp commons-dbcp.jar commons-dbcp-1.1.jar
+	java-pkg_jar-from commons-pool commons-pool.jar commons-pool-1.1.jar
+	java-pkg_jar-from bytecode
+}
+
+src_compile() {
+	#ANT_OPTS="${ANT_OPTS} -Xmx512m"
+	eant package-biojava package-biojava package-demos package-apps #$(use_doc javadocs-all)
+}
+
+src_install() {
+	java-pkg_newjar ant-build/biojava.jar ${PN}.jar
+	java-pkg_newjar ant-build/apps.jar ${PN}-apps.jar
+	java-pkg_newjar ant-build/demos.jar ${PN}-demos.jar
+	#use doc && java-pkg_dojavadoc ant-build/doc/{biojava,apps,demos}
+	use source && java-pkg_dosrc {src,apps,demos}/org
+}
+
+src_test() {
+	java-pkg_jar-from junit-4 junit.jar junit-4.4.jar
+	ANT_TASKS="ant-junit4" eant runtests
+}
diff --git a/sci-biology/biojava/metadata.xml b/sci-biology/biojava/metadata.xml
new file mode 100644
index 000000000000..0a18364544e8
--- /dev/null
+++ b/sci-biology/biojava/metadata.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<herd>java</herd>
+</pkgmetadata>