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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
AUTOTOOLS_AUTORECONF=yes
inherit flag-o-matic eutils perl-module webapp autotools
DESCRIPTION="Analyze restriction enzyme data, draw gen. maps, population genomics"
HOMEPAGE="http://creskolab.uoregon.edu/stacks"
SRC_URI="http://creskolab.uoregon.edu/stacks/source/${P}.tar.gz"
LICENSE="GPL-3"
# SLOT="0" # webapp ebuilds do not set SLOT
KEYWORDS=""
IUSE=""
DEPEND="
>=sci-libs/htslib-1.3.1
dev-cpp/sparsehash
sci-biology/samtools:*
sci-biology/bamtools
sci-biology/gmap" # Source code for both GMAP and GSNAP
RDEPEND="${DEPEND}
dev-lang/perl
>=dev-lang/php-5
dev-perl/DBD-mysql"
src_prepare(){
sed -e 's/SUBDIRS = htslib/SUBDIRS = /' -i Makefile.am || die
mycppflags=`pkg-config --cflags htslib` # is blocked by bug #601366
sed -e "s#-I./htslib/htslib#-I${mycppflags}#" -i configure.ac || die
eautoreconf
}
src_configure() {
econf --enable-bam --enable-sparsehash
webapp_src_preinst
sed -i 's#/usr/lib/libbam.a#-lbam#' Makefile || die
}
src_compile(){
rm -rf htslib # zap bundled htslib-1.3.1
emake DESTDIR="${D}"
}
src_install() {
emake install DESTDIR="${D}"
mydoc="Changes README TODO INSTALL"
perl-module_src_install DESTDIR="${D}"
webapp_src_install || die "Failed running webapp_src_install"
}
pkg_postinst() {
webapp_pkg_postinst || die "webapp_pkg_postinst failed"
}
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