commit: a4f1661dd0ed743fd5ea4e21edc558c83fbc5dd6 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sat May 9 22:55:35 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sat May 9 22:55:35 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a4f1661d
sci-biology/wise: version bump, new HOMEPAGE, SRC_URI, does not compile, the former patches need to be updated as well Package-Manager: portage-2.2.18 sci-biology/wise/ChangeLog | 10 ++++++ sci-biology/wise/metadata.xml | 5 +++ sci-biology/wise/wise-2.4.1.ebuild | 74 ++++++++++++++++++++++++++++++++++++++ 3 files changed, 89 insertions(+) diff --git a/sci-biology/wise/ChangeLog b/sci-biology/wise/ChangeLog new file mode 100644 index 0000000..7bbe629 --- /dev/null +++ b/sci-biology/wise/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/wise +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*wise-2.4.1 (09 May 2015) + + 09 May 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> +metadata.xml, + +wise-2.4.1.ebuild: + sci-biology/wise: version bump, new HOMEPAGE, SRC_URI, does not compile, the + former patches need to be updated as well diff --git a/sci-biology/wise/metadata.xml b/sci-biology/wise/metadata.xml new file mode 100644 index 0000000..f17a827 --- /dev/null +++ b/sci-biology/wise/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/wise/wise-2.4.1.ebuild b/sci-biology/wise/wise-2.4.1.ebuild new file mode 100644 index 0000000..d7d88b6 --- /dev/null +++ b/sci-biology/wise/wise-2.4.1.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/wise-2.4.0_alpha.ebuild,v 1.6 2015/04/19 10:02:55 ago Exp $ + +EAPI=5 + +inherit eutils toolchain-funcs versionator + +DESCRIPTION="Genewise, promoterwise: align protein HMMs to DNA for CDS predictions" +HOMEPAGE="http://www.ebi.ac.uk/~birney/wise2"; +SRC_URI="http://www.ebi.ac.uk/~birney/${PN}2/${PN}$(delete_version_separator 3).tar.gz" +#SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="" +IUSE="doc static-libs" + +RDEPEND="~sci-biology/hmmer-2.3.2" +DEPEND=" + ${RDEPEND} + app-shells/tcsh + dev-lang/perl + virtual/latex-base" + +S="${WORKDIR}"/${PN}$(delete_version_separator 3) + +#src_prepare() { +# epatch \ +# "${FILESDIR}"/${P}-glibc-2.10.patch \ +# "${FILESDIR}"/${P}-cflags.patch +# cd "${S}"/docs || die +# cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die +# cat wise2api.tex temp.tex apiend.tex > api.tex || die +# epatch "${FILESDIR}"/${PN}-api.tex.patch +#} + +src_compile() { + emake \ + -C src \ + CC="$(tc-getCC)" \ + all + if use doc; then + cd "${S}"/docs || die + for i in api appendix dynamite wise2 wise3arch; do + latex ${i} || die + latex ${i} || die + dvips ${i}.dvi -o || die + done + fi +} + +src_test() { + cd "${S}"/src || die + WISECONFIGDIR="${S}/wisecfg" emake test +} + +src_install() { + dobin "${S}"/src/bin/* "${S}"/src/dynlibsrc/testgendb + use static-libs && \ + dolib.a \ + "${S}"/src/base/libwisebase.a \ + "${S}"/src/dynlibsrc/libdyna.a \ + "${S}"/src/models/libmodel.a + + insinto /usr/share/${PN} + doins -r "${S}"/wisecfg + + if use doc; then + insinto /usr/share/doc/${PF} + doins "${S}"/docs/*.ps + fi + newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file" +}
