From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 947AC138334 for ; Wed, 20 Feb 2019 12:50:26 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id A8136E0828; Wed, 20 Feb 2019 12:50:25 +0000 (UTC) Received: from smtp.gentoo.org (mail.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 7DF95E0828 for ; Wed, 20 Feb 2019 12:50:24 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 553E9335CC0 for ; Wed, 20 Feb 2019 12:50:23 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id F222A44B for ; Wed, 20 Feb 2019 12:50:20 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1550667003.44e3ae771a3aa414d91c4687cb707b2d16b32ff7.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/canu/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/canu/canu-9999.ebuild sci-biology/canu/metadata.xml X-VCS-Directories: sci-biology/canu/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 44e3ae771a3aa414d91c4687cb707b2d16b32ff7 X-VCS-Branch: master Date: Wed, 20 Feb 2019 12:50:20 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 6f5de935-e6bb-46b3-a800-80062d9b2200 X-Archives-Hash: 29374e3e08b1d24100be7ef8683ee321 commit: 44e3ae771a3aa414d91c4687cb707b2d16b32ff7 Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Wed Feb 20 12:50:03 2019 +0000 Commit: Martin Mokrejs fold natur cuni 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 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 @@ + + + + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + + + sci-biology@gentoo.org + Gentoo Biology Project + +