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diff --git a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
new file mode 100644
index 000000000000..e4c4d95288fd
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+++ b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools flag-o-matic toolchain-funcs
+
+DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
+# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12
+HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
+SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	!sci-biology/allpaths
+	!sci-biology/vaal"
+DEPEND="
+	${RDEPEND}
+	dev-libs/boost:="
+
+PATCHES=(
+	"${FILESDIR}/${P}_fix-buildsystem.patch"
+	"${FILESDIR}/${P}_remove-namespace-std.patch"
+)
+
+pkg_pretend() {
+	# as of release 44849, GCC 4.7.0 (or higher) is required
+	# seems pre gcc-4.7 users must stay with:
+	# ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz
+	if [[ ${MERGE_TYPE} != binary ]]; then
+		tc-is-gcc && [[ $(gcc-version) < 4.7 ]] && \
+			die "You need to use gcc >4.7"
+	fi
+}
+
+pkg_setup() {
+	if ! tc-has-openmp; then
+		ewarn "OpenMP is not available in your current selected compiler"
+
+		if tc-is-clang; then
+			ewarn "OpenMP support in sys-devel/clang is provided by sys-libs/libomp,"
+			ewarn "which you will need to build ${CATEGORY}/${PN} with USE=\"openmp\""
+		fi
+
+		die "need openmp capable compiler"
+	fi
+}
+
+src_prepare() {
+	default
+
+	eautoreconf
+}