commit: f7194dde6bb1e013487400d22fa0a663ca909338 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Jan 7 22:13:13 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Jan 7 22:13:13 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f7194dde
Initial ebuild --- sci-biology/tigr-closure/ChangeLog | 10 ++++ sci-biology/tigr-closure/metadata.xml | 9 +++ .../tigr-closure/tigr-closure-20080106.ebuild | 68 ++++++++++++++++++++++ 3 files changed, 87 insertions(+) diff --git a/sci-biology/tigr-closure/ChangeLog b/sci-biology/tigr-closure/ChangeLog new file mode 100644 index 0000000..eba3b60 --- /dev/null +++ b/sci-biology/tigr-closure/ChangeLog @@ -0,0 +1,10 @@ +# 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 <[email protected]> + +tigr-closure-20080106.ebuild, +metadata.xml: + initial ebuild + diff --git a/sci-biology/tigr-closure/metadata.xml b/sci-biology/tigr-closure/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/tigr-closure/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>[email protected]</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 new file mode 100644 index 0000000..068dde9 --- /dev/null +++ b/sci-biology/tigr-closure/tigr-closure-20080106.ebuild @@ -0,0 +1,68 @@ +# 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 + # +}
