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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit 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/${P}.tar.gz"
LICENSE="GPL-3"
# SLOT="0" # webapp ebuilds do not set SLOT
KEYWORDS=""
# No rule to make target test
RESTRICT="test"
DEPEND="
>=sci-libs/htslib-1.3.1:0
dev-cpp/sparsehash
sci-biology/samtools:*
sci-biology/bamtools
sci-biology/gmap" # Source code for both GMAP and GSNAP
RDEPEND="${DEPEND}
dev-lang/perl
>=dev-lang/php-5
dev-perl/DBD-mysql"
PATCHES=(
"${FILESDIR}/${PN}-make-install.patch"
)
src_prepare(){
default
#mycppflags=`pkg-config --cflags htslib` # is blocked by bug #601366
if [ -z "$mycppflags" ]; then mycppflags="."; fi
sed -e "s#-I./htslib/htslib#-I/usr/include/bam -I${mycppflags}#" -i configure.ac || die
eautoreconf
}
src_configure() {
econf
webapp_src_preinst
sed -e 's#/usr/lib/libbam.a#-lbam#;#./htslib/libhts.a#-lhts#' -i Makefile || die
}
src_install() {
emake install DESTDIR="${ED}"
mydoc="Changes README TODO INSTALL"
perl-module_src_install DESTDIR="${ED}"
webapp_src_install || die "Failed running webapp_src_install"
}
pkg_postinst() {
webapp_pkg_postinst || die "webapp_pkg_postinst failed"
}
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