commit: 44e3ae771a3aa414d91c4687cb707b2d16b32ff7 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Feb 20 12:50:03 2019 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Feb 20 12:50:03 2019 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=44e3ae77
sci-biology/canu: add live package of a new tool Package-Manager: Portage-2.3.61, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz> sci-biology/canu/canu-9999.ebuild | 50 +++++++++++++++++++++++++++++++++++++++ sci-biology/canu/metadata.xml | 12 ++++++++++ 2 files changed, 62 insertions(+) diff --git a/sci-biology/canu/canu-9999.ebuild b/sci-biology/canu/canu-9999.ebuild new file mode 100644 index 000000000..bef85d20f --- /dev/null +++ b/sci-biology/canu/canu-9999.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit java-pkg-2 git-r3 + +DESCRIPTION="Fork of a wgs-assembler for Oxfordnanopore and PacBio sequences" +HOMEPAGE="http://canu.readthedocs.io/en/latest"; +EGIT_REPO_URI="https://github.com/marbl/canu.git"; + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="" + +RDEPEND=" + >=virtual/jre-1.8:* + dev-lang/perl + virtual/perl-File-Path + sci-visualization/gnuplot + " +# =sci-biology/mhap-2.1.3 if we unbundle it +DEPEND="${RDEPEND} + >=virtual/jdk-1.8:* + dev-java/ant-core + " + +# Perl 5.12.0, or File::Path 2.08 +# Java SE 8 +# https://github.com/marbl/MHAP uses Apache maven +S="${WORKDIR}"/"${P}" + +# contains bundled mhap-2.1.3.jar, kmer, pbutgcns, FALCON + +src_compile(){ + cd src || die + emake +} + +src_install(){ + # installs + # /usr/bin + # /usr/lib/libcanu.a + # /usr/lib/site_perl/canu + # /usr/share/java/classes/mhap-2.1.3.jar + rm -rf Linux-amd64/obj + insinto /usr + doins -r Linux-amd64/{bin,lib,share} +} diff --git a/sci-biology/canu/metadata.xml b/sci-biology/canu/metadata.xml new file mode 100644 index 000000000..138cb7705 --- /dev/null +++ b/sci-biology/canu/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>
