commit: ea2ae88794c9415404bdad68dacedb3522e10d24 Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Sat Jan 15 11:01:45 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Sat Jan 15 11:01:45 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ea2ae887
sci-biology/ncbi-vdb: 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/ncbi-vdb/metadata.xml | 12 ++++++++ sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild | 45 +++++++++++++++++++++++++++++ 2 files changed, 57 insertions(+) diff --git a/sci-biology/ncbi-vdb/metadata.xml b/sci-biology/ncbi-vdb/metadata.xml new file mode 100644 index 000000000..138cb7705 --- /dev/null +++ b/sci-biology/ncbi-vdb/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>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild b/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild new file mode 100644 index 000000000..167e2a8c3 --- /dev/null +++ b/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild @@ -0,0 +1,45 @@ +# 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=" NCBI SRA ( Sequence Read Archive )" +HOMEPAGE="https://github.com/ncbi/ncbi-vdb"; +SRC_URI="https://github.com/ncbi/ncbi-vdb/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +# Sandbox error: tries to access files from within deleted dir in compile phase +KEYWORDS="" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND="${PYTHON_DEPS} + sci-libs/hdf5 + sci-biology/ngs +" +RDEPEND="${DEPEND}" + +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 +}
