commit: ab1f6781e9c576702f48058e7d9c86676973b693 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Mon May 25 19:04:23 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Mon May 25 19:04:23 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ab1f6781
sci-biology/AlignGraph: new package Package-Manager: portage-2.2.18 sci-biology/AlignGraph/AlignGraph-9999.ebuild | 53 +++++++++++++++++++++++++++ sci-biology/AlignGraph/ChangeLog | 9 +++++ sci-biology/AlignGraph/metadata.xml | 9 +++++ 3 files changed, 71 insertions(+) diff --git a/sci-biology/AlignGraph/AlignGraph-9999.ebuild b/sci-biology/AlignGraph/AlignGraph-9999.ebuild new file mode 100644 index 0000000..b7e2866 --- /dev/null +++ b/sci-biology/AlignGraph/AlignGraph-9999.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit toolchain-funcs + +if [ "$PV" == "9999" ]; then + inherit git-r3 +fi + +DESCRIPTION="Asssemble contigs/scaffolds using related reference sequence" +HOMEPAGE="https://github.com/baoe/AlignGraph + http://bioinformatics.oxfordjournals.org/content/30/12/i319.long"; +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/baoe/AlignGraph.git"; + KEYWORDS="" +else + SRC_URI="" + KEYWORDS="" +fi + +LICENSE="Artistic-2" +SLOT="0" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + sci-biology/blat + sci-biology/bowtie" + +# AlignGraph runs the alignment steps with BLAT and Bowtie2 automatically, but both +# need to be installed on the system. AlignGraph’s run time is currently 23–57 min +# per million aligned reads. In the performance tests of this study, the memory usage +# was 36–50 GB, and it stays <100 GB even for entire mammalian genomes. These requirements +# are more moderate than those of most de novo assemblers (Luo et al., 2012). + +# 8 threads are hardcoded. Currently users cannot make changes to this, since this is +# a moderate choice for either single CPU machines (overhead for parallelization would +# not be too large) or multiple CPU machines. Another reason is, the bottleneck for the +# runtime is usually from BLAT, no matter how many threads there are for Bowtie2. +src_compile(){ + cd AlignGraph || die + $(tc-getCXX) ${CXXFLAGS} -o AlignGraph AlignGraph.cpp -lpthread + cd ../Eval-AlignGraph || die + $(tc-getCXX) ${CXXFLAGS} -o Eval-AlignGraph Eval-AlignGraph.cpp -lpthread +} + +src_install(){ + dobin AlignGraph/AlignGraph Eval-AlignGraph/Eval-AlignGraph + dodoc README.md +} diff --git a/sci-biology/AlignGraph/ChangeLog b/sci-biology/AlignGraph/ChangeLog new file mode 100644 index 0000000..d6c0196 --- /dev/null +++ b/sci-biology/AlignGraph/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/AlignGraph +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*AlignGraph-9999 (25 May 2015) + + 25 May 2015; Martin Mokrejs <[email protected]> + +AlignGraph-9999.ebuild, +metadata.xml: + sci-biology/AlignGraph: new package diff --git a/sci-biology/AlignGraph/metadata.xml b/sci-biology/AlignGraph/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/AlignGraph/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>
