Initial ebuild

4 files changed, 88 insertions, 0 deletions

diff --git a/sci-biology/tigr-closure/ChangeLog b/sci-biology/tigr-closure/ChangeLog
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+# ChangeLog for sci-biology/tigr-closure
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*tigr-closure-20080106 (07 Jan 2015)
+
+  07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +tigr-closure-20080106.ebuild, +metadata.xml:
+  initial ebuild
+
diff --git a/sci-biology/tigr-closure/Manifest b/sci-biology/tigr-closure/Manifest
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+++ b/sci-biology/tigr-closure/Manifest
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+DIST tigr-closure-svn-20080106.tar.gz 25760145 SHA256 60e474beb7e408c3c47633b2bf029ff9fde05840a10b01c875164e68811b6c5f
diff --git a/sci-biology/tigr-closure/metadata.xml b/sci-biology/tigr-closure/metadata.xml
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+++ b/sci-biology/tigr-closure/metadata.xml
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+<?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/tigr-closure/tigr-closure-20080106.ebuild b/sci-biology/tigr-closure/tigr-closure-20080106.ebuild
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index 000000000..068dde987
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+++ b/sci-biology/tigr-closure/tigr-closure-20080106.ebuild
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+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit perl-module
+
+DESCRIPTION="TIGR closure tools for the assembly/finishing stage of DNA sequencing projects"
+HOMEPAGE="http://tigr-closure.sourceforge.net/"
+# http://tigr-closure.svn.sourceforge.net/tigr-closure/
+SRC_URI="tigr-closure-svn-20080106.tar.gz"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-lang/perl"
+RDEPEND=""
+
+src_compile() {
+	cd TIGR
+	# install the two *.pm files into our perl path?
+	cd ..
+
+	# Closure Work Order Processing (CWP - CLOVER)
+	# clover and oats
+	cd ${WORKDIR}/CWPSystem/trunk/
+	# needs TIGR/EUIDService.pm in PERL paths
+	make dist
+	# how to install the files from install/ ?
+	cd ../..
+	
+	# 
+	cd ScaffoldMgmt/trunk
+	make dist
+	# FIXME: unpack the .tar file into image during src_install()
+	cd ../..
+
+	# awfull
+	cd ClosureQC/trunk/
+	mkdir sandbox
+	${SANDBOX}=${WORKDIR}/sandbox
+	# have ./src/, ./doc, ./install, ./test/work/drivers, ./test/work/getqc, ./test/tmp
+	cd test
+	# ...
+	cd ../../..
+
+	# 
+	cd ClosureReactionSystem/trunk
+	make BUILD=true
+	cd ../..
+
+	# some Java servlet?
+	cd AserverConsoleEJB3Hibernate
+	# huh?
+	cd ../..
+}
+
+src_install() {
+	cd ${WORKDIR}/SequenceTiling
+	dobin trunk/src/*.pl
+	cd trunk/src/TIGR/SequenceTiling/
+	myinst="DESTDIR=${D}"
+	perl-module_src_install
+	#
+}