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# Copyright 1999-2009 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI="2"
inherit toolchain-funcs flag-o-matic webapp
DESCRIPTION="The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath"
HOMEPAGE="http://genome.ucsc.edu"
SRC_URI="http://hgdownload.cse.ucsc.edu/admin/jksrc.v${PV}.zip"
LICENSE="blat"
# webapp ebuilds do not set SLOT
KEYWORDS="~amd64 ~x86"
IUSE="server"
DEPEND="app-arch/unzip
virtual/mysql
server? ( virtual/httpd-cgi )" # TODO: test with other webservers
RDEPEND="${DEPEND}"
S="${WORKDIR}/kent"
src_prepare() {
use server && webapp_src_preinst
sed -i -e 's/-Werror//' \
-e "s/CC=gcc/CC=$(tc-getCC) ${CFLAGS}/" \
src/inc/common.mk || die
find -name makefile -or -name cgi_build_rules.mk \
| xargs sed -i -e 's/-${USER}//g' -e 's/-$(USER)//g' || die
}
src_compile() {
export MACHTYPE=${MACHTYPE/-*/} \
BINDIR="${WORKDIR}/destdir/opt/${PN}/bin" \
SCRIPTS="${WORKDIR}/destdir/opt/${PN}/cluster/scripts" \
ENCODE_PIPELINE_BIN="${WORKDIR}/destdir/opt/${PN}/cluster/data/encode/pipeline/bin" \
PATH="${BINDIR}:${PATH}" \
STRIP="echo 'skipping strip' "
export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none"
# use mysql &&
export MYSQLLIBS="${ROOT}usr/lib/mysql/libmysqlclient.a -lz -lssl" \
MYSQLINC="${ROOT}usr/include/mysql"
use server && export DOCUMENTROOT="${WORKDIR}/destdir/${MY_HTDOCSDIR}" \
CGI_BIN="${WORKDIR}/destdir/${MY_HTDOCSDIR}/cgi-bin"
mkdir -p "$BINDIR" "$SCRIPTS" "$ENCODE_PIPELINE_BIN" || die
use server && mkdir -p "$CGI_BIN" "$DOCUMENTROOT"
emake -C src clean || die
emake -C src/lib || die
emake -C src/jkOwnLib || die
emake -C src/utils/stringify || die
emake -j1 -C src/hg utils || die
emake -j1 -C src utils || die
emake -C src blatSuite userApps || die
if use server; then
emake -j1 -C src/hg || die
emake -j1 -C src || die
fi
}
src_install() {
cp -a "${WORKDIR}"/destdir/* "${D}" || die
# dolib.a src/lib/*.a src/hg/altSplice/lib/x86_64/libSpliceGraph.a
echo "PATH=/opt/${PN}/bin" > "${S}/99${PN}"
doenvd "${S}/99${PN}"
# TODO
use server && webapp_postinst_txt en src/product/README.QuickStart
use server && webapp_src_install
insinto "/opt/${PN}/include"
doins src/inc/*.h
insinto "/usr/share/${PN}"
doins -r src/product
keepdir "/usr/share/doc/${PF}"
find -name 'README*' -or -name '*.doc' | grep -v test | cpio -padv "${D}/usr/share/doc/${PF}" || die
}
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