commit: 9eb2c98e084ad39a175118774bad2e0fd587057d Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Mar 23 21:13:39 2014 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Mar 23 21:13:39 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9eb2c98e
sci-biology/Atlas2: a skeleton for a new package, needs help from ruby team --- sci-biology/Atlas2/Atlas2-1.4.3.ebuild | 41 ++++++++++++++++++++++++++++++++++ sci-biology/Atlas2/ChangeLog | 10 +++++++++ sci-biology/Atlas2/metadata.xml | 9 ++++++++ 3 files changed, 60 insertions(+) diff --git a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild new file mode 100644 index 0000000..7e2049d --- /dev/null +++ b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +USE_RUBY="ruby19 ruby20" + +inherit ruby-fakegem + +DESCRIPTION="Variant analysis tools (true SNPs, insertions, deletions) from whole exome capture sequencing (WECS)" +HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas2"; +SRC_URI="http://downloads.sourceforge.net/project/atlas2/Atlas2_v1.4.3.zip"; + +LICENSE="BSD" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="dev-lang/ruby + sci-biology/samtools + sci-biology/blat + sci-biology/phrap + sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/all/"${PN}"_v"${PV}" + +src_compile(){ + cd SOLiD-SNP-caller || die + emake + + cd ../vcfPrinter + # TODO: install the *.rb files + + cd ../Atlas-Indel2 + # TODO: install the *.rb and files in lib/ + + cd ../Atlas-SNP2 + # TODO: install +} diff --git a/sci-biology/Atlas2/ChangeLog b/sci-biology/Atlas2/ChangeLog new file mode 100644 index 0000000..65bee22 --- /dev/null +++ b/sci-biology/Atlas2/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/Atlas2 +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*Atlas2-1.4.3 (23 Mar 2014) + + 23 Mar 2014; Martin Mokrejs <[email protected]> + +Atlas2-1.4.3.ebuild, +metadata.xml: + a skeleton for a new package, needs help from ruby team + diff --git a/sci-biology/Atlas2/metadata.xml b/sci-biology/Atlas2/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/Atlas2/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>
