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 45A2F1382DE for ; Thu, 30 Jun 2016 18:06:23 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 91C8F1400F; Thu, 30 Jun 2016 18:06:20 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 439EA1400F for ; Thu, 30 Jun 2016 18:06:19 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id ACCF6340E09 for ; Thu, 30 Jun 2016 18:06:18 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id C693B241B for ; Thu, 30 Jun 2016 18:06:16 +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: <1467309963.50c01592d588fb2dadc5e4ca17aefc2943cb9f96.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/Atlas/Atlas-2005.ebuild X-VCS-Directories: sci-biology/Atlas/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 50c01592d588fb2dadc5e4ca17aefc2943cb9f96 X-VCS-Branch: master Date: Thu, 30 Jun 2016 18:06:16 +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: ab377773-6e8d-456f-90d7-3dbe83a7b918 X-Archives-Hash: d9530c7b481c7e65babc802d9081b365 commit: 50c01592d588fb2dadc5e4ca17aefc2943cb9f96 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Jun 30 18:06:03 2016 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Jun 30 18:06:03 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=50c01592 sci-biology/Atlas: fix Makefiles at least, will need to unbundle some gzstream library too Package-Manager: portage-2.2.28 sci-biology/Atlas/Atlas-2005.ebuild | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/sci-biology/Atlas/Atlas-2005.ebuild b/sci-biology/Atlas/Atlas-2005.ebuild index c95df06..4806d1c 100644 --- a/sci-biology/Atlas/Atlas-2005.ebuild +++ b/sci-biology/Atlas/Atlas-2005.ebuild @@ -4,6 +4,8 @@ EAPI=5 +inherit toolchain-funcs + DESCRIPTION="Atlas Whole Genome Assembly Suite" HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-whole-genome-assembly-suite" SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas-src.tgz" @@ -17,12 +19,16 @@ IUSE="" DEPEND="dev-libs/boost" RDEPEND="${DEPEND}" -S="${WORKDIR}"/atlas-src +S="${WORKDIR}"/atlas-src/CBT + +src_prepare(){ + sed -e "s/^CC =/CC = $(tc-getCC)/" -e "s/^GCC =/GCC = $(tc-getCXX)/" -i Makefile || die + sed -e "s/^GCC =/GCC = $(tc-getCXX)/" -i ../CBTApps/Makefile.in || die +} src_compile(){ # install headers, bins and libs into CBT_DEVEL_USER, then compile apps - cd src || die - emake CBT_DEVEL_DIR="${S}"/CBT CBT_INSTALL_DIR="${D}" + emake CBT_DEVEL_DIR="${S}" CBT_INSTALL_DIR="${D}" cd ../CBTApps || die - emake CBT_DEVEL_DIR="${S}"/CBT CBT_INSTALL_DIR="${D}" + emake CBT_DEVEL_DIR="${S}" CBT_INSTALL_DIR="${D}" }