commit: 54f544dd58ebf9e5ac9e4ccdeedeb32688fd3365 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Mon Jan 18 12:42:29 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> 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 <andrewammerlaan <AT> 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.* +}
