From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 0770758973 for ; Thu, 11 Feb 2016 20:49:56 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 6798CE083A; Thu, 11 Feb 2016 20:49:55 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id F1543E083A for ; Thu, 11 Feb 2016 20:49:54 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 3A010340AA7 for ; Thu, 11 Feb 2016 20:49:53 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 4757A8F8 for ; Thu, 11 Feb 2016 20:49:51 +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: <1455223633.62afc0eb5df8a6b490373a37d801ff4e7d373613.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/grass/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/grass/grass-20130628.ebuild sci-biology/grass/metadata.xml X-VCS-Directories: sci-biology/grass/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 62afc0eb5df8a6b490373a37d801ff4e7d373613 X-VCS-Branch: master Date: Thu, 11 Feb 2016 20:49:51 +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-Archives-Salt: f9a815ca-10b7-4a26-8e4c-6526d26e7c38 X-Archives-Hash: b1f97fc2cead6f6039bce25badfd8e03 commit: 62afc0eb5df8a6b490373a37d801ff4e7d373613 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Feb 11 20:47:13 2016 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Feb 11 20:47:13 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=62afc0eb sci-biology/grass: new package, see bugs at github.com Package-Manager: portage-2.2.26 sci-biology/grass/grass-20130628.ebuild | 39 +++++++++++++++++++++++++++++++++ sci-biology/grass/metadata.xml | 12 ++++++++++ 2 files changed, 51 insertions(+) diff --git a/sci-biology/grass/grass-20130628.ebuild b/sci-biology/grass/grass-20130628.ebuild new file mode 100644 index 0000000..9744012 --- /dev/null +++ b/sci-biology/grass/grass-20130628.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Scaffold next-generation sequencing assemblies" +HOMEPAGE="https://github.com/AlexeyG/GRASS" +SRC_URI="https://github.com/AlexeyG/GRASS/archive/master.zip -> grass-20130628.zip + https://tud-scaffolding.googlecode.com/files/GRASS%20manual.pdf -> grass_manual.pdf" +# EGIT_REPO_URI="https://github.com/AlexeyG/GRASS.git" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +# some IBM development CPLEX library? +# ilcplex/ilocplex.h: No such file or directory +DEPEND="sci-biology/bamtools + sci-biology/ncbi-tools++" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/GRASS-master + +src_prepare(){ + sed -e 's#/data/bio/alexeygritsenk/apps/include/ncbi-tools++#/usr/include/ncbi-tools++#' -i Makefile.config || die + sed -e 's#/data/bio/alexeygritsenk/apps/include/#/usr/include/bamtools#' -i Makefile.config || die + sed -e 's#/data/bio/alexeygritsenk/apps/lib#/usr/lib64#' -i Makefile.config || die +} + +src_compile(){ + emake all +} + +src_install(){ + dodoc "${DISTDIR}"/grass_manual.pdf manual/manual.tex + dobin bin/* +} diff --git a/sci-biology/grass/metadata.xml b/sci-biology/grass/metadata.xml new file mode 100644 index 0000000..1699e58 --- /dev/null +++ b/sci-biology/grass/metadata.xml @@ -0,0 +1,12 @@ + + + + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + + + sci-biology@gentoo.org + Gentoo Biology Project + +