sci-biology/vague-bin: new java binary package

Package-Manager: portage-2.2.7

5 files changed, 68 insertions, 0 deletions

diff --git a/sci-biology/vague-bin/ChangeLog b/sci-biology/vague-bin/ChangeLog
new file mode 100644
index 000000000..30734b2ec
--- /dev/null
+++ b/sci-biology/vague-bin/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/vague-bin
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*vague-bin-1.0.5 (08 Jan 2015)
+
+  08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +files/vague.patch,
+  +metadata.xml, +vague-bin-1.0.5.ebuild:
+  sci-biology/vague-bin: new java binary package
diff --git a/sci-biology/vague-bin/Manifest b/sci-biology/vague-bin/Manifest
new file mode 100644
index 000000000..8f80714d7
--- /dev/null
+++ b/sci-biology/vague-bin/Manifest
@@ -0,0 +1 @@
+DIST vague-1.0.5.tar.gz 19109369 SHA256 7144bef4a5c8ccb3d0e6b27201a506e1cfa25812fb9bbe54842dc910100c5907 SHA512 4b676099dd51f45b80c9afbdf17d3eef07f847576437aa592a35ff5e81f54b6c6004c9bd3af15aa944339fa5f78745630d9ea45ea4de984c51d2c7d58667f6b7 WHIRLPOOL fbe8f4174949921f899fbfe1c8acfc8442425eba34b7b2d56b297e622e748085df2c6e34503a976489d36467750c90b9c0c4aa7b52fd9d02731ba3b1679d93f9
diff --git a/sci-biology/vague-bin/files/vague.patch b/sci-biology/vague-bin/files/vague.patch
new file mode 100644
index 000000000..61f4c1a59
--- /dev/null
+++ b/sci-biology/vague-bin/files/vague.patch
@@ -0,0 +1,8 @@
+--- vague.ori	2015-01-08 13:31:31.755604378 +0100
++++ vague	2015-01-08 13:31:49.525604424 +0100
+@@ -1,4 +1,4 @@
+ echo "Starting Vague, please wait..."
+ export VAGUE_DIR=`dirname $0`
+ export PATH=$PATH:$VAGUE_DIR
+-java -Xmx3750m -jar `dirname $0`/vague.jar $*
++java -Xmx3750m -jar /usr/share/vague-bin/lib/vague.jar $*
diff --git a/sci-biology/vague-bin/metadata.xml b/sci-biology/vague-bin/metadata.xml
new file mode 100644
index 000000000..2bc893037
--- /dev/null
+++ b/sci-biology/vague-bin/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
new file mode 100644
index 000000000..479d88a2c
--- /dev/null
+++ b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2
+
+[ "$PV" == "9999" ] && inherit git-2
+
+DESCRIPTION="GUI for Velvet de novo assembler"
+HOMEPAGE="http://www.vicbioinformatics.com/software.vague.shtml"
+
+if [ "$PV" == "9999" ]; then
+	EGIT_REPO_URI="https://github.com/Victorian-Bioinformatics-Consortium/vague"
+	KEYWORDS=""
+else
+	SRC_URI="http://www.vicbioinformatics.com/vague-"${PV}".tar.gz"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=">=virtual/jre-1.5
+	sci-biology/velvet
+	sci-biology/velvetk"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/vague-"${PV}"
+
+src_prepare(){
+	epatch "${FILESDIR}"/vague.patch
+}
+
+src_install(){
+	dobin vague
+	java-pkg_dojar vague.jar || die
+}