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 7D20E1382C5 for ; Sat, 21 Apr 2018 17:17:32 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 9237CE0848; Sat, 21 Apr 2018 17:17:31 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (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 5ECC9E0848 for ; Sat, 21 Apr 2018 17:17:30 +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 3D557335C74 for ; Sat, 21 Apr 2018 17:17:29 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 688B427C for ; Sat, 21 Apr 2018 17:17:27 +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: <1524331032.5bcbca87122d15ab6ae31547021b65c872cef1c5.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/salmon/salmon-0.6.0.ebuild sci-biology/salmon/salmon-0.9.1.ebuild sci-biology/salmon/salmon-9999.ebuild X-VCS-Directories: sci-biology/salmon/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 5bcbca87122d15ab6ae31547021b65c872cef1c5 X-VCS-Branch: master Date: Sat, 21 Apr 2018 17:17:27 +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: 20b7dee7-220d-4b82-9d97-c5cca7606133 X-Archives-Hash: 4b4c910a1504aa5a8b5f1c3858ff9034 commit: 5bcbca87122d15ab6ae31547021b65c872cef1c5 Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Sat Apr 21 17:17:12 2018 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sat Apr 21 17:17:12 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5bcbca87 sci-biology/salmon: document install procedure issues The building procedure is still a mess. https://github.com/COMBINE-lab/salmon/issues/19 Package-Manager: Portage-2.3.28, Repoman-2.3.9 .../{salmon-0.6.0.ebuild => salmon-0.9.1.ebuild} | 4 +-- sci-biology/salmon/salmon-9999.ebuild | 29 +++++++++++++++++++--- 2 files changed, 27 insertions(+), 6 deletions(-) diff --git a/sci-biology/salmon/salmon-0.6.0.ebuild b/sci-biology/salmon/salmon-0.9.1.ebuild similarity index 84% rename from sci-biology/salmon/salmon-0.6.0.ebuild rename to sci-biology/salmon/salmon-0.9.1.ebuild index f88310f95..34a425403 100644 --- a/sci-biology/salmon/salmon-0.6.0.ebuild +++ b/sci-biology/salmon/salmon-0.9.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2018 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -14,8 +14,6 @@ SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="" -PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch ) - DEPEND="dev-libs/boost:0 dev-libs/jemalloc dev-cpp/tbb" diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild index 4acc02e71..4f48644c6 100644 --- a/sci-biology/salmon/salmon-9999.ebuild +++ b/sci-biology/salmon/salmon-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2018 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -14,12 +14,35 @@ LICENSE="GPL-3" SLOT="0" IUSE="" -PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch ) - DEPEND="dev-libs/boost:0 dev-libs/jemalloc dev-cpp/tbb" RDEPEND="${DEPEND}" +# https://github.com/COMBINE-lab/salmon/issues/19 +# +# contains bundled copies of https://github.com/jemalloc/jemalloc +# https://github.com/gabime/spdlog +# https://github.com/efficient/libcuckoo +# https://github.com/greg7mdp/sparsepp +# https://github.com/COMBINE-lab/RapMap +# https://github.com/Kingsford-Group/libgff +# sci-libs/io_lib +# +# https://github.com/COMBINE-lab/salmon/issues/19#issuecomment-144721158 +# modified bwa copy +# +# and maybe more + +src_configure(){ + local mycmakeargs=( + "-DBOOST_ROOT=${EPREFIX}/usr" + "-DTBB_INSTALL_DIR=${EPREFIX}/usr" + "-DCMAKE_INSTALL_PREFIX=${EPREFIX}/usr" + ) + # BUG: the configure step run automatically curl download of 3rd-party stuff + # https://github.com/COMBINE-lab/salmon/issues/19 + cmake-utils_src_configure +} src_install() { cmake-utils_src_install