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| author |   Andrew Ammerlaan <andrewammerlaan@gentoo.org> | 2022-01-15 12:01:45 +0100 |
|---|---|---|
| committer | Andrew Ammerlaan <andrewammerlaan@gentoo.org> | 2022-01-15 12:01:45 +0100 |
| commit | ea2ae88794c9415404bdad68dacedb3522e10d24 (patch) | |
| tree | 4cbb58c17d875203d654475b4d5551537e800535 /sci-biology/ncbi-vdb | |
| parent | sci-biology/ngs: add new dep of sra-tools (diff) | |
| download | sci-ea2ae88794c9415404bdad68dacedb3522e10d24.tar.gz sci-ea2ae88794c9415404bdad68dacedb3522e10d24.tar.bz2 sci-ea2ae88794c9415404bdad68dacedb3522e10d24.zip | |
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@gentoo.org>
Diffstat (limited to 'sci-biology/ncbi-vdb')
| -rw-r--r-- | sci-biology/ncbi-vdb/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/ncbi-vdb/metadata.xml | 12 | ||||
| -rw-r--r-- | sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild | 45 |
3 files changed, 58 insertions, 0 deletions
diff --git a/sci-biology/ncbi-vdb/Manifest b/sci-biology/ncbi-vdb/Manifest new file mode 100644 index 000000000..6e69589e6 --- /dev/null +++ b/sci-biology/ncbi-vdb/Manifest @@ -0,0 +1 @@ +DIST ncbi-vdb-2.11.2.tar.gz 26543426 BLAKE2B a0acdeefa5e4fadfcc304d33b29be5ae937630fb74b13674e1e7ea8dd4cd71048a1374803fcc6e2248fa4ecb9be93945fcd567f40159748eb86f0fdc98bf6aff SHA512 c3b9e582c9faccd637d5718bbaac49603c993be9234c7bd561ab84cabb9a2d60508822211871c9cd2d3bd42fbb059e5f72194d9e28e126c21ccf70ea8ab6b5b0 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>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</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 +} |