reinit the tree, so we can have metadata

4 files changed, 132 insertions, 0 deletions

diff --git a/sci-biology/goby/Manifest b/sci-biology/goby/Manifest
new file mode 100644
index 000000000000..678f78558ab7
--- /dev/null
+++ b/sci-biology/goby/Manifest
@@ -0,0 +1,9 @@
+DIST goby_1.9.7.3-deps.zip 19959489 SHA256 3932c61f001fc1d06ef298043d5206041e47175fa28d755efd01148de35b567a SHA512 a077e18d6bb7603522108de2b3c50d1b7a281c9e1a8d5d78c85b660285d743baf7b52ceaea44903a5a27adfa80ea5823d5aaa47a3f2ec426e7ddb17fd67a477d WHIRLPOOL 35f09d7a64c32358e6f4c4f8002e2569f2b79a019c9f111c5dd046860c26905baf8de8ee6bc7ebdd90b96c390f0202a4cd0487d4e84522b8f304bf9739696ba6
+DIST goby_1.9.7.3-src.zip 15642000 SHA256 fe32a6720fcc0858811e40b744c9bcfffbb6cf277be50102446ff8798fd9ab24 SHA512 f213908e745e6c6d86895412f3ad14a8e0f2f3fbaba9205bffd7415982fc53181ca0b03b543063d0cbcd87f881d1b58eedb38a5090fa7ac20bdc513e54f83dd5 WHIRLPOOL c5f0d7d21624983f9e6f95c65eb477a21b3d5749cca53dab537060c8ce0facf6b4cc1f2705af025088fb6fd325539907a53691f42fbdaa9f3044fae75bcaa8ce
+DIST goby_1.9.8.1-deps.zip 20820943 SHA256 eb11916408a7978a1e90967783b8167b96c6d0dd60ae58cf1dab915a519d1bbb SHA512 16cf79e2dab8cfc62f9d012b88b0d81e712e67cf2f70582969624a019863f21ee20a4ce0517d5b74782d8d200318451e3f889fb967c6935e896d526d2a6fc02e WHIRLPOOL 00ec51b2999cb34b725a48ad0456d23c40a952272f58b558c8fb0cc3e086a89a11bd6440bddddb0ea7b9bbcadeb05078161b02617ee5c55baf388aa73802b187
+DIST goby_1.9.8.1-src.zip 15748880 SHA256 e2489a815a38bd10b1ec59b4e262a023f97994d9953f97bcc6571cadd05919c3 SHA512 68e772f1a60d1c78d2b08ee203f462e6ac19a46124d25ac1bd7c69065d8122ce6dbfbd3cc6aa287b13b11d5442e9b41609463a8391ffe037249655a212284ff0 WHIRLPOOL 05277c80d0b9235ea3835fef0d34afca3aacbf1ff84624997d19ab749b8fd4b12c0bda2bf519f2ed031575edf2dac5f312835c67d7ded33a44b2767675c4f4cc
+EBUILD goby-1.9.7.3-r1.ebuild 1531 SHA256 02a64cdc71e17f81811ed3a38fb15b6615029e69514d97ff9cc487782235a6ba SHA512 b8a99a082b6453db69ce740912d823e2f5b0009ded8082fa66955882e1b88fc86c92b374a17d0d8d9870624119ba2509f8cefb3e5165b87a22cd540e9c40c768 WHIRLPOOL 70d9c9a5410eb6b8342ff626d3302d9d6207e97da01a42a732be513229c0a388a62fcf3a987959a57229bb5808e5a126e5fdc71de795e4e84558b41b457c3ca9
+EBUILD goby-1.9.8.1-r1.ebuild 1531 SHA256 02a64cdc71e17f81811ed3a38fb15b6615029e69514d97ff9cc487782235a6ba SHA512 b8a99a082b6453db69ce740912d823e2f5b0009ded8082fa66955882e1b88fc86c92b374a17d0d8d9870624119ba2509f8cefb3e5165b87a22cd540e9c40c768 WHIRLPOOL 70d9c9a5410eb6b8342ff626d3302d9d6207e97da01a42a732be513229c0a388a62fcf3a987959a57229bb5808e5a126e5fdc71de795e4e84558b41b457c3ca9
+MISC ChangeLog 2835 SHA256 f4476a07537c9d74f7c8fb826ed97e3ac4b97508f5503beb4a57d8fec25e6f1e SHA512 aa7b596952270647cf86c2dc8e52afc5945d34faeca3747e3684977322a19441a24f788a406eb2854f907fea115062ad64fbc806e244ab510f755bab4babdd22 WHIRLPOOL b2aa112d59fb739ff85ad6f1244872207fce4328092b82cdf59138cf9112b7abed3c70fe156ef52c873b239079e853b3d789d5829e0760bec3d0e59f18da8800
+MISC ChangeLog-2015 615 SHA256 f8f65e9e4b465958c847c3f2147e833db9726130ee5a8fedec8f3909f36f6a79 SHA512 315255594170894eb8d4b8806bdca67e16696f314ee861324dcc64ebfa09745ddbe7294eb149e2f75390d72af2d3bf3b92a0f512a86c4cf556b42e8f96ba9651 WHIRLPOOL 42b4423e82917c6a0131250c33ea837e4afb4e6d547bb2dd0d3d84686d7e332fc45d8376732aad8b10cd8fb37fb8950aa1516ef02b74d56cc6ba33256a0ea340
+MISC metadata.xml 330 SHA256 b95d24f3bf9019f4b6b7fd35a160e4cd8d0fe3002b7c71828683538666978d30 SHA512 7d7909e5632e5d2c18241237d5e06501e50d2d1fe07a618e8a028fbdd17bc2a420e23bead1529c6cfe76a82fdb04fd636b911230b57722ad9bd16e796baeb87e WHIRLPOOL bbb96e4a38e1fef9c9f1acc80f6b895134f533ef9d6623584f247637e657c520a8937d002978fd8f7b652feda2321b7c1d194a3b27d8bdc28fabde57bedbf033
diff --git a/sci-biology/goby/goby-1.9.7.3-r1.ebuild b/sci-biology/goby/goby-1.9.7.3-r1.ebuild
new file mode 100644
index 000000000000..9cab1b56d54e
--- /dev/null
+++ b/sci-biology/goby/goby-1.9.7.3-r1.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=4
+
+ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby"
+EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf-java,fastutil,log4j,jsap,commons-configuration,commons-math-2"
+EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar"
+
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+#inherit java-pkg-2 java-ant-2 subversion
+inherit java-pkg-2 java-ant-2
+
+MY_P="${PN}_${PV}"
+
+DESCRIPTION="A DNA sequencing data management framework"
+HOMEPAGE="http://campagnelab.org/software/goby/"
+SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip
+	http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip"
+
+LICENSE="GPL-3 LGPL-3"
+SLOT="0"
+IUSE="+cpp"
+KEYWORDS="~amd64 ~x86"
+
+COMMON_DEPS="dev-java/commons-logging
+	dev-java/commons-lang:2.1
+	dev-java/commons-io:1
+	dev-java/protobuf-java:0
+	dev-java/fastutil:0
+	dev-java/log4j
+	dev-java/jsap
+	dev-java/commons-configuration
+	dev-java/commons-math:2"
+DEPEND=">=virtual/jdk-1.6
+	${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.6
+	${COMMON_DEPS}
+	cpp? ( ~sci-biology/goby-cpp-${PV} )"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	sed -i '/sge/ d' build.xml || die
+	java-pkg-2_src_prepare
+}
+
+src_install() {
+	java-pkg_dojar goby*.jar
+	java-pkg_dolauncher goby --jar goby.jar
+
+	insinto /usr/share/${PN}
+	doins -r python
+	dodoc CHANGES.txt
+}
diff --git a/sci-biology/goby/goby-1.9.8.1-r1.ebuild b/sci-biology/goby/goby-1.9.8.1-r1.ebuild
new file mode 100644
index 000000000000..9cab1b56d54e
--- /dev/null
+++ b/sci-biology/goby/goby-1.9.8.1-r1.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=4
+
+ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby"
+EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf-java,fastutil,log4j,jsap,commons-configuration,commons-math-2"
+EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar"
+
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+#inherit java-pkg-2 java-ant-2 subversion
+inherit java-pkg-2 java-ant-2
+
+MY_P="${PN}_${PV}"
+
+DESCRIPTION="A DNA sequencing data management framework"
+HOMEPAGE="http://campagnelab.org/software/goby/"
+SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip
+	http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip"
+
+LICENSE="GPL-3 LGPL-3"
+SLOT="0"
+IUSE="+cpp"
+KEYWORDS="~amd64 ~x86"
+
+COMMON_DEPS="dev-java/commons-logging
+	dev-java/commons-lang:2.1
+	dev-java/commons-io:1
+	dev-java/protobuf-java:0
+	dev-java/fastutil:0
+	dev-java/log4j
+	dev-java/jsap
+	dev-java/commons-configuration
+	dev-java/commons-math:2"
+DEPEND=">=virtual/jdk-1.6
+	${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.6
+	${COMMON_DEPS}
+	cpp? ( ~sci-biology/goby-cpp-${PV} )"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	sed -i '/sge/ d' build.xml || die
+	java-pkg-2_src_prepare
+}
+
+src_install() {
+	java-pkg_dojar goby*.jar
+	java-pkg_dolauncher goby --jar goby.jar
+
+	insinto /usr/share/${PN}
+	doins -r python
+	dodoc CHANGES.txt
+}
diff --git a/sci-biology/goby/metadata.xml b/sci-biology/goby/metadata.xml
new file mode 100644
index 000000000000..a1e19f7893ca
--- /dev/null
+++ b/sci-biology/goby/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <use>
+    <flag name="cpp">Compile C/C++ API</flag>
+  </use>
+</pkgmetadata>