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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
inherit java-pkg-2 eutils java-ant-2
DESCRIPTION="Perl-based wrapper around java apps to quality control FASTA/FASTQ sequence files"
HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"${PV}"_source.zip"
LICENSE="GPL-3+"
SLOT="0"
KEYWORDS=""
IUSE=""
DEPEND="sci-biology/picard
sci-libs/jhdf5
>=virtual/jre-1.5:*"
RDEPEND="${DEPEND}
dev-lang/perl
>=virtual/jdk-1.5:*
dev-java/ant-core"
S="${WORKDIR}"/FastQC
src_prepare(){
cp "${FILESDIR}"/build.xml . || die
}
src_compile(){
ant || die
}
src_install(){
dobin fastqc run_fastqc.bat
dodoc README.txt RELEASE_NOTES.txt
# There is no fastqc.jar. The output from the compilation is the set of
# .class files (a jar file is just a zip file full of .class files). All
# you need to copy out is the contents of the bin subdirectory, the rest of
# the download you can discard.
#
# jbzip2-0.9.jar comes from https://code.google.com/p/jbzip2
#
# ignore the sam-1.103.jar and rely on /usr/share/picard/lib/sam.jar from sci-biology/picard
# The sam-1.103.jar library comes from
# http://sourceforge.net/projects/picard/files/sam-jdk/. Note that there is
# a newer version of this codebase at https://github.com/samtools/htsjdk but
# that FastQC is NOT yet compatible with the updated API (this will probably
# happen in a future release). This library is needed to read SAM/BAM
# format files.
# cisd-jhdf5.jar should be provided by sci-libs/jhdf5
}
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