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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
inherit git-r3 toolchain-funcs
DESCRIPTION="A tool set for short variant discovery in genetic sequence data"
HOMEPAGE="https://github.com/atks/vt
http://genome.sph.umich.edu/wiki/vt"
EGIT_REPO_URI="https://github.com/atks/vt.git"
LICENSE="MIT"
SLOT="0"
KEYWORDS=""
IUSE="pdf"
DEPEND=""
RDEPEND="${DEPEND}
pdf? ( dev-texlive/texlive-latex || ( dev-texlive/texlive-basic ) )"
# >=sci-libs/htslib-1.3.2
# dev-cpp/tclap
# sci-libs/libsvm
# dev-libs/libpcre
# https://github.com/atks/Rmath
# The 3rd party stuff is bundled because they have special modifications that
# I made for vt, so it is probably not a good idea to depend on installed components.
# For example TCLAP is modified partially, libsvm has some minor input/output format changes,
# Rmath has the header inclusion to always generate the .a object file
# Compiles statically bundled version of htslib and Rmath, only libpcre2 is dynamically linked
src_prepare(){
sed -e "s/= -O3/= ${CFLAGS}/" -i Makefile || die
sed -e 's/^CXX = /CXX ?= /' -i Makefile || die
sed -e "s/-g -Wall -O2/${CFLAGS}/" -i lib/htslib/Makefile || die
sed -e "s/= gcc/= $(tc-getCC)/" -i lib/htslib/Makefile || die
sed -e "s/gcc -g -O3/$(tc-getCC) ${CFLAGS}/" -i lib/pcre2/Makefile || die
sed -e "s/-Wall -O3 -fPIC/${CXXFLAGS} -fPIC/" -i lib/libsvm/Makefile || die
# # TODO zap bundled version of:
# # lib/htslib (version 1.3)
# # lib/tclap
# # lib/Rmath
# # lib/libsvm
# # lib/pcre2
}
src_install(){
dobin vt
}
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