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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
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="~amd64 ~x86"
IUSE="doc static-libs"
RDEPEND="sci-biology/hmmer:2"
DEPEND="
${RDEPEND}
dev-lang/perl
virtual/latex-base
dev-libs/glib"
S="${WORKDIR}"/${PN}$(delete_version_separator 3)
src_prepare() {
epatch "${FILESDIR}"/wise-2.2.0-glibc-2.10.patch
epatch "${FILESDIR}"/wise-2.4.1-cflags.patch
epatch "${FILESDIR}"/01_welcome-csh.patch
epatch "${FILESDIR}"/02_isnumber.patch
epatch "${FILESDIR}"/03_doc-nodycache.patch
epatch "${FILESDIR}"/04_wise2-pdflatex-update.patch
# the two below are already in wise-2.2.0-glibc-2.10.patch wise-2.4.1-cflags.patch
#epatch "${FILESDIR}"/06_getline.patch
#epatch "${FILESDIR}"/07_ld--as-needed.patch
epatch "${FILESDIR}"/08_mayhem.patch
epatch "${FILESDIR}"/09_dnal-add-return-statement.patch
epatch "${FILESDIR}"/11_consistent_manual_dates.patch
# cd "${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
#
# eventually, zap bundled but modified version of hmmer-2?
# This is not recommended, because sean and I diverged a while back on indexing
# strategies. At some point I will need to port the later HMMer into Wise2.
# rm -rf src/HMMer2 || die "Cannot zap bundled hmmer-2 sources"
# sed -e "s#HMMER_INCLUDE = ../HMMer2/#HMMER_INCLUDE = ${EPREFIX}/usr/include/hmmer2#" -i src/makefile || die
# sed -e "s#HMMER_LIBS.* = ../HMMer2/#HMMER_LIBS = ${EPREFIX}/usr/$(get_libdir)"#" -i src/makefile || die
# TODO: change eventual callers of the hmmer-2 binaries?
# ./test_data/*.{HMM,hmm}
# ./src/test/*.{HMM,hmm}
# ./src/perl/makelib.pl
#for e in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmpfam hmmsearch; do \
# # append '2' to the filename in "$e"
#done
}
src_compile() {
emake \
-C src \
CC="$(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"
}
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