1 files changed, 48 insertions, 0 deletions
diff --git a/sci-biology/sra-tools/sra-tools-2.11.3.ebuild b/sci-biology/sra-tools/sra-tools-2.11.3.ebuild
new file mode 100644
index 000000000..57c5b881e
--- /dev/null
+++ b/sci-biology/sra-tools/sra-tools-2.11.3.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="NCBI Sequence Read Archive (SRA) sratoolkit"
+HOMEPAGE="https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi https://github.com/ncbi/sra-tools"
+SRC_URI="https://github.com/ncbi/sra-tools/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+# Fix ncbi-vdb first
+KEYWORDS=""
+
+DEPEND="
+	sys-libs/zlib
+	app-arch/bzip2
+	dev-libs/libxml2:2=
+	sci-libs/hdf5
+	sci-biology/ngs
+	sci-biology/ncbi-vdb
+"
+
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/sra-tools-${PV}"
+
+src_configure() {
+	# this is some non-standard configure script
+	./configure \
+		--with-ngs-sdk-prefix=/usr/ngs/ngs-sdk \
+		--with-hdf5-prefix=/usr \
+		|| die
+}
+
+src_install() {
+	dodir /usr/include
+	dodir /etc/profile.d
+	# Hard way around hard coded paths
+	find . -type f -exec sed -i \
+		-e "s:/usr/local:${ED}/usr:g" \
+		-e "s:/etc:${ED}/etc:g" \
+		-e "s:/usr/lib:${ED}/usr/lib:g" \
+		-e "s:/usr/include:${ED}/usr/include:g" \
+		-e "s:setup.py -q install:setup.py install --root="${D}":g" \
+		{} \; || die
+	default
+}