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 58F2A1382C5 for ; Mon, 18 Jan 2021 12:43:00 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 8C785E0788; Mon, 18 Jan 2021 12:42:59 +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 7197AE0788 for ; Mon, 18 Jan 2021 12:42:59 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (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 5476D340FDD for ; Mon, 18 Jan 2021 12:42:58 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id A75DB3A6 for ; Mon, 18 Jan 2021 12:42:56 +0000 (UTC) From: "Andrew Ammerlaan" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Andrew Ammerlaan" Message-ID: <1610973749.54f544dd58ebf9e5ac9e4ccdeedeb32688fd3365.andrewammerlaan@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/wcd/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/wcd/wcd-0.6.3.ebuild sci-biology/wcd/wcd-0.6.3_p20180430.ebuild X-VCS-Directories: sci-biology/wcd/ X-VCS-Committer: andrewammerlaan X-VCS-Committer-Name: Andrew Ammerlaan X-VCS-Revision: 54f544dd58ebf9e5ac9e4ccdeedeb32688fd3365 X-VCS-Branch: master Date: Mon, 18 Jan 2021 12:42:56 +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: a409b5a8-942c-433b-8afa-cf1c0f5d8b6a X-Archives-Hash: 275b554e99f5fe2486ca40e35b865d8a commit: 54f544dd58ebf9e5ac9e4ccdeedeb32688fd3365 Author: Andrew Ammerlaan riseup net> AuthorDate: Mon Jan 18 12:42:29 2021 +0000 Commit: Andrew Ammerlaan riseup net> CommitDate: Mon Jan 18 12:42:29 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=54f544dd sci-biology/wcd: fix fetch Package-Manager: Portage-3.0.13, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> sci-biology/wcd/wcd-0.6.3.ebuild | 62 ------------------------------ sci-biology/wcd/wcd-0.6.3_p20180430.ebuild | 48 +++++++++++++++++++++++ 2 files changed, 48 insertions(+), 62 deletions(-) diff --git a/sci-biology/wcd/wcd-0.6.3.ebuild b/sci-biology/wcd/wcd-0.6.3.ebuild deleted file mode 100644 index d4b797608..000000000 --- a/sci-biology/wcd/wcd-0.6.3.ebuild +++ /dev/null @@ -1,62 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -AUTOTOOLS_AUTORECONF=true - -inherit autotools-utils flag-o-matic multilib - -DESCRIPTION="EST sequence clustering: d2 function, edit distance, common word heuristics" -HOMEPAGE="http://code.google.com/p/wcdest/" -SRC_URI="http://wcdest.googlecode.com/files/wcd-express-${PV}.tar.gz -> ${P}.tar.gz - http://www.bioinf.wits.ac.za/~scott/wcd.html - http://www.bioinf.wits.ac.za/~scott/wcd.pdf" - -S="${WORKDIR}"/wcd-express-"${PV}" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="doc mpi threads" - -# This code (0.4.1 at least) has been tested using LAMMPI (RedHat, Suse, -# MacOS X), MPICH (Ubuntu) and MVAPICH (Suse) -DEPEND="mpi? ( sys-cluster/mpich2 )" -RDEPEND="" - -PATCHES=( - "${FILESDIR}"/${P}-ldflags.patch - "${FILESDIR}"/${P}-impl-decl.patch - ) - -src_prepare() { - rm -r src/*o src/.deps || die - autotools-utils_src_prepare -} - -src_configure(){ - local myeconfargs=() - use mpi && myeconfargs+=( --enable-mpi ) - - use threads && myeconfargs+=( --enable-pthreads ) - - autotools-utils_src_configure -} - -src_compile() { - autotools-utils_src_compile - use doc && autotools-utils_src_compile pdf info html -} - -src_install() { - use doc && HTML_DOCS=( doc/wcd.html doc/wcd.pdf doc/wcd.texi ) - autotools-utils_src_install PREFIX=/usr LIBDIR="${D}"usr/$(get_libdir) - dodoc "${DISTDIR}"/wcd.* -} - -# consider providing the EMBOSS wrapper for wcd -# https://code.google.com/p/wcdest/downloads/detail?name=wcd_emboss_wrap_001.tar.gz - -# also consider ESTsim -# https://code.google.com/p/wcdest/downloads/detail?name=estsim_distrib.tar.gz&can=2&q= diff --git a/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild b/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild new file mode 100644 index 000000000..740deddba --- /dev/null +++ b/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +COMMIT="aee525029bb661b633097e989c6fe2eaa93d2def" + +inherit multilib + +DESCRIPTION="EST sequence clustering: d2 function, edit distance, common word heuristics" +HOMEPAGE="https://shaze.github.io/wcdest/" +SRC_URI="https://github.com/shaze/wcdest/archive/${COMMIT}.tar.gz -> ${P}.tar.gz + http://www.bioinf.wits.ac.za/~scott/wcd.html + http://www.bioinf.wits.ac.za/~scott/wcd.pdf" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="" + +IUSE="doc mpi threads" + +# This code (0.4.1 at least) has been tested using LAMMPI (RedHat, Suse, +# MacOS X), MPICH (Ubuntu) and MVAPICH (Suse) +DEPEND="mpi? ( sys-cluster/mpich2 )" + +PATCHES=( + "${FILESDIR}"/${PN}-0.6.3-ldflags.patch + "${FILESDIR}"/${PN}-0.6.3-impl-decl.patch +) + +S="${WORKDIR}/${PN}est-${COMMIT}/code" + +src_configure(){ + econf \ + $(use_enable mpi) \ + $(use_enable threads pthreads) +} + +src_compile() { + default + use doc && emake pdf info html +} + +src_install() { + use doc && HTML_DOCS=( doc/wcd.html doc/wcd.pdf doc/wcd.texi ) + emake install PREFIX=/usr LIBDIR="${D}"usr/$(get_libdir) + dodoc "${DISTDIR}"/wcd.* +}