commit: c6e01bee05d3b6a88b906f5e6a4c93892ef43bcd Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Jan 17 22:47:07 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Jan 17 22:47:07 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c6e01bee
sci-biology/nextclip: new package It does not do a proper alignment so no surprise it does not work well (see github issues from several users). Also, the nextclip binary triggers a QA issue (opened as github issue #22) due to writable and executable sections. Package-Manager: Portage-2.3.19, Repoman-2.3.6 sci-biology/nextclip/metadata.xml | 12 +++++++++ sci-biology/nextclip/nextclip-1.3.1.ebuild | 41 ++++++++++++++++++++++++++++++ 2 files changed, 53 insertions(+) diff --git a/sci-biology/nextclip/metadata.xml b/sci-biology/nextclip/metadata.xml new file mode 100644 index 000000000..138cb7705 --- /dev/null +++ b/sci-biology/nextclip/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/nextclip/nextclip-1.3.1.ebuild b/sci-biology/nextclip/nextclip-1.3.1.ebuild new file mode 100644 index 000000000..3efbb61c6 --- /dev/null +++ b/sci-biology/nextclip/nextclip-1.3.1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="Split Illumina Nextera long mate-pairs" +HOMEPAGE="https://github.com/richardmleggett/nextclip + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928519"; +SRC_URI="https://github.com/richardmleggett/nextclip/archive/NextClip_v1.3.1.tar.gz"; + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + >=dev-lang/R-2.12.2 + >=sci-biology/bwa-0.6.1 + dev-texlive/texlive-latex" + +S="${WORKDIR}"/"${PN}"-NextClip_v"${PV}" + +src_prepare(){ + default + sed -e 's/$(ARCH)//;s/$(MACFLAG)//' -i Makefile || die + sed -e "s/CC=gcc/$(tc-getCC)/;s/-Wall -O3/${CFLAGS}/" -i Makefile || die +} + +src_compile(){ + emake all +} + +src_install(){ + dobin bin/nextclip + insinto /usr/share/"${PN}" + doins scripts/* + dodoc nextclipmanual.pdf README.md +}
