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 E29E8138ACF for ; Sat, 14 Feb 2015 16:17:46 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 1541AE0991; Sat, 14 Feb 2015 16:17:46 +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 7DB4CE0991 for ; Sat, 14 Feb 2015 16:17:44 +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 652FB3407F3 for ; Sat, 14 Feb 2015 16:17:43 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 4DA3811BFE for ; Sat, 14 Feb 2015 16:17:41 +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: <1423930482.aeab720fe4e2a73d39d79fa4570cd71219f256f6.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/mip-scaffolder/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/mip-scaffolder/ChangeLog sci-biology/mip-scaffolder/metadata.xml sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild X-VCS-Directories: sci-biology/mip-scaffolder/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: aeab720fe4e2a73d39d79fa4570cd71219f256f6 X-VCS-Branch: master Date: Sat, 14 Feb 2015 16:17:41 +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: 32f19e30-3c91-4278-ad12-79f7e759f7fb X-Archives-Hash: 29a32aa3c1fdbd1ada9e48a0d5e9aaa3 commit: aeab720fe4e2a73d39d79fa4570cd71219f256f6 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Sat Feb 14 16:14:42 2015 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sat Feb 14 16:14:42 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=aeab720f new package Package-Manager: portage-2.2.15 --- sci-biology/mip-scaffolder/ChangeLog | 9 ++++++ sci-biology/mip-scaffolder/metadata.xml | 9 ++++++ .../mip-scaffolder/mip-scaffolder-0.6.ebuild | 32 ++++++++++++++++++++++ 3 files changed, 50 insertions(+) diff --git a/sci-biology/mip-scaffolder/ChangeLog b/sci-biology/mip-scaffolder/ChangeLog new file mode 100644 index 0000000..0cba1df --- /dev/null +++ b/sci-biology/mip-scaffolder/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/mip-scaffolder +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*mip-scaffolder-0.6 (14 Feb 2015) + + 14 Feb 2015; Martin Mokrejs +metadata.xml, + +mip-scaffolder-0.6.ebuild: + new package diff --git a/sci-biology/mip-scaffolder/metadata.xml b/sci-biology/mip-scaffolder/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/mip-scaffolder/metadata.xml @@ -0,0 +1,9 @@ + + + + sci-biology + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + + diff --git a/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild b/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild new file mode 100644 index 0000000..525ecbe --- /dev/null +++ b/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION="Scaffold contigs using ABI Solid or Illumina mate pair info" +HOMEPAGE="http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder" +SRC_URI="http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/"${P}".tar.gz" + +LICENSE="mip-scaffolder" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="sci-libs/lemon + sci-mathematics/lpsolve + dev-lang/perl" +RDEPEND="${DEPEND}" + +src_prepare(){ + sed -e 's:/home/user/lp-solve/:/usr/include/lpsolve/:; s:/home/user/lemon/:/usr/include/lemon:; s:/home/user/mip-scaffolder-0.6/:/usr/bin:' -i Makefile + find . -name Makefile | while read f; do sed -e "s:CC=g++:CC=$(tc-getCXX):; s:CFLAGS=-Wall -g -O9:CFLAGS=${CFLAGS}:" -i $f; done + sed -e 's:$(LPSOLVEROOT)/liblpsolve55.a:-llpsolve55:' -i split-scaffold/Makefile +} + +src_install(){ + dobin combine-scaffold/combine-scaffold filter-mappings/filter-mappings split-scaffold/split-scaffold write-scaffold/write-scaffold scripts/*.pl scripts/*.sh + dodoc README +}