commit: 4efdba16fdc718fde4b8679fb805cb382df46fef Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Apr 1 15:04:25 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Apr 1 15:04:25 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4efdba16
sci-biology/seq_crumbs: new package The fix to setup.py to respect DESTDIR is probably not ideal. Needs a fix to avoid file collisions. Package-Manager: Portage-2.3.27, Repoman-2.3.9 sci-biology/seq_crumbs/metadata.xml | 12 +++++++ sci-biology/seq_crumbs/seq_crumbs-0.1.9.ebuild | 46 ++++++++++++++++++++++++++ 2 files changed, 58 insertions(+) diff --git a/sci-biology/seq_crumbs/metadata.xml b/sci-biology/seq_crumbs/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/seq_crumbs/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/seq_crumbs/seq_crumbs-0.1.9.ebuild b/sci-biology/seq_crumbs/seq_crumbs-0.1.9.ebuild new file mode 100644 index 000000000..94ce00a94 --- /dev/null +++ b/sci-biology/seq_crumbs/seq_crumbs-0.1.9.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 eutils + +DESCRIPTION="Filter, split and trim NGS sequence data" +HOMEPAGE="https://github.com/JoseBlanca/seq_crumbs"; +SRC_URI="https://github.com/JoseBlanca/"${PN}"/archive/v"${PV}".tar.gz"; + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND=" + >=sci-biology/biopython-1.60 + >=sci-biology/pysam-0.8 + >=dev-python/rpy-2 + dev-python/matplotlib + dev-python/configobj + dev-python/toolz" +RDEPEND="${DEPEND}" + +# TODO fix file collisions +# * Detected file collision(s): +# * +# * /usr/share/man/man1/index.1.bz2 +# * /usr/share/man/man1/install.1.bz2 +# * +# * Searching all installed packages for file collisions... +# * +# * Press Ctrl-C to Stop +# * +# * sys-apps/coreutils-8.29:0::gentoo +# * /usr/share/man/man1/install.1.bz2 +# * +# * media-libs/netpbm-10.76.00:0::gentoo +# * /usr/share/man/man1/index.1.bz2 +src_prepare(){ + sed -e "s#sys.prefix#os.getenv('ED')+'/usr/'#" -i setup.py || die + default +}
