commit: 7286213decca43e6185a611dc357a71557fd84c9 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Jan 7 20:39:33 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Jan 7 20:39:33 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7286213d
sci-biology/ICC: initial ebuild, perl installation steps need to be fixed --- sci-biology/ICC/ChangeLog | 9 ++++++ sci-biology/ICC/ICC-2.0.1.ebuild | 61 ++++++++++++++++++++++++++++++++++++++++ sci-biology/ICC/metadata.xml | 9 ++++++ 3 files changed, 79 insertions(+) diff --git a/sci-biology/ICC/ChangeLog b/sci-biology/ICC/ChangeLog new file mode 100644 index 0000000..cd415fd --- /dev/null +++ b/sci-biology/ICC/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/ICC +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*ICC-2.0.1 (07 Jan 2015) + + 07 Jan 2015; Martin Mokrejs <[email protected]> +ICC-2.0.1.ebuild: + initial ebuild, perl installation steps need to be fixed + diff --git a/sci-biology/ICC/ICC-2.0.1.ebuild b/sci-biology/ICC/ICC-2.0.1.ebuild new file mode 100644 index 0000000..5e5fb5c --- /dev/null +++ b/sci-biology/ICC/ICC-2.0.1.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit perl-module + +DESCRIPTION="Error corrector for Roche/454 and IonTorrent data with indel and carryforward, SNP and haplotype calling" +HOMEPAGE="http://indra.mullins.microbiol.washington.edu/ICC"; +SRC_URI="http://indra.mullins.microbiol.washington.edu/cgi-bin/ICC/info.cgi?ID=ICC_v2.0.1.zip -> ICC_v2.0.1.zip" + +LICENSE="" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="dev-lang/perl + sci-biology/ncbi-tools++" +RDEPEND="${DEPEND}" + +S="${WORKDIR}" + +src_install(){ + dobin Scripts/*.pl + dodoc README.txt + + # BUG: does not work + cd Scripts/lib || die + perl-module_src_install DESTDIR="${D}" *.pm Parallel/ForkManager.pm # install into @INC path + +} + +# testing: Blast/Linux/LICENSE OK +# testing: Example/exampleReads.fas OK +# testing: Example/exampleReads.qual OK +# testing: Example/exampleReference.fas OK +# testing: README.md OK +# testing: README.txt OK +# testing: Scripts/ OK +# testing: Scripts/CC.pl OK +# testing: Scripts/HIC.pl OK +# testing: Scripts/IC.pl OK +# testing: Scripts/alignRegion.pl OK +# testing: Scripts/config.pl OK +# testing: Scripts/lib/ OK +# testing: Scripts/lib/.DS_Store OK +# testing: Scripts/lib/Parallel/ OK +# testing: Scripts/lib/Parallel/ForkManager.pm OK +# testing: Scripts/lib/paths.pm OK +# testing: Scripts/lib/seqAlign.pm OK +# testing: Scripts/lib/utils.pm OK +# testing: Scripts/ntFreq.pl OK +# testing: Scripts/readQualFilter.pl OK +# testing: Scripts/retrieveRegion.pl OK +# testing: Scripts/retrieveWindows.pl OK +# testing: Scripts/runBLAST.pl OK +# testing: Scripts/runICC.pl OK +# testing: Scripts/uniqueReads.pl OK +# testing: VersionHistory.txt OK + diff --git a/sci-biology/ICC/metadata.xml b/sci-biology/ICC/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/ICC/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>
