diff options
Diffstat (limited to 'sci-biology/sra-tools')
| -rw-r--r-- | sci-biology/sra-tools/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/sra-tools/metadata.xml | 12 | ||||
| -rw-r--r-- | sci-biology/sra-tools/sra-tools-2.11.3.ebuild | 48 |
3 files changed, 61 insertions, 0 deletions
diff --git a/sci-biology/sra-tools/Manifest b/sci-biology/sra-tools/Manifest new file mode 100644 index 000000000..1ece174af --- /dev/null +++ b/sci-biology/sra-tools/Manifest @@ -0,0 +1 @@ +DIST sra-tools-2.11.3.tar.gz 9098150 BLAKE2B 852db3b1d1409b37e3a8f36d0a64f5480ba8c85b86efa8f1d9524a5a8a4c2763aa6970739aa06a0821be576b920946784ab9a9ce1af3e6ceaa54da9b743a0434 SHA512 070ab552df1789d37e970e1c9ac2ce7ac6b39ce7833a999aabee4baef553a29a4bfcbdb21be00f4b5d8a55013bcf88b46c839a124dde704b4a371b234c05609f diff --git a/sci-biology/sra-tools/metadata.xml b/sci-biology/sra-tools/metadata.xml new file mode 100644 index 000000000..138cb7705 --- /dev/null +++ b/sci-biology/sra-tools/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/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 +} |