1 files changed, 54 insertions, 0 deletions
diff --git a/sci-biology/vcflib/vcflib-1.0.3.ebuild b/sci-biology/vcflib/vcflib-1.0.3.ebuild
new file mode 100644
index 000000000..d4cf1e02f
--- /dev/null
+++ b/sci-biology/vcflib/vcflib-1.0.3.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake toolchain-funcs
+
+DESCRIPTION="VCF/BED utils, Genotype Phenotype Association Toolkit (GPAT++)"
+HOMEPAGE="https://github.com/vcflib/vcflib"
+SRC_URI="https://github.com/vcflib/vcflib/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT-with-advertising"
+SLOT="0"
+# No proper release tarball for this release yet
+KEYWORDS=""
+IUSE="openmp"
+
+DEPEND="
+	sys-libs/zlib
+	sci-libs/htslib
+	sci-biology/tabixpp
+"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	cmake_src_prepare
+	sed -e "s/^CXX = g++/CXX = $(tc-getCXX)/" -i Makefile || die
+	sed -e "s/^CXXFLAGS = -O3/CXXFLAGS = ${CXXFLAGS}/" -i Makefile || die
+	# openmp detection stolen from velvet-1.2.10.ebuild
+	if use openmp; then
+		if [[ $(tc-getCXX) =~ g++ ]]; then
+			local eopenmp=-fopenmp
+		elif [[ $(tc-getCXX) =~ cxx ]]; then
+			local eopenmp=-openmp
+			sed -e "s/-fopenmp/${eopenmp}/" -i Makefile || die
+		else
+			elog "Cannot detect compiler type so not setting openmp support"
+		fi
+	fi
+}
+
+src_compile(){
+	mycmakeargs=(
+		-DOPENMP="$(use_enable openmp)"
+		-DHTSLIB_LOCAL=ON
+	)
+	cmake_src_compile
+}
+#
+# src_install(){
+# 	dobin bin/*
+# 	dolib lib/* # install libvcflib.a
+# 	dodoc README.md
+# }