[gentoo-commits] proj/sci:master commit in: sci-biology/ngs/

[Andrew Ammerlaan]

commit:     2d893e4f6dd9835a92f032448ebafe0cf6877760
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 15 11:01:14 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sat Jan 15 11:01:14 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2d893e4f

sci-biology/ngs: add new dep of sra-tools

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/ngs/metadata.xml      | 12 +++++++++++
 sci-biology/ngs/ngs-2.11.2.ebuild | 42 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 54 insertions(+)

diff --git a/sci-biology/ngs/metadata.xml b/sci-biology/ngs/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/ngs/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mmokrejs@×××××××××××××××.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@g.o</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+</pkgmetadata>

diff --git a/sci-biology/ngs/ngs-2.11.2.ebuild b/sci-biology/ngs/ngs-2.11.2.ebuild
new file mode 100644
index 000000000..d398d6f96
--- /dev/null
+++ b/sci-biology/ngs/ngs-2.11.2.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit python-single-r1
+
+DESCRIPTION="NGS Language Bindings "
+HOMEPAGE="https://github.com/ncbi/ngs"
+SRC_URI="https://github.com/ncbi/ngs/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}
+	sci-biology/bamtools
+"
+RDEPEND="${DEPEND}
+	virtual/jre:*
+"
+
+src_configure() {
+	# this is some non-standard configure script
+	./configure || 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
+}