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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
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${PV}.zip"
LICENSE="blat"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="+mysql +server static-libs"
REQUIRED_USE="server? ( mysql )"
WEBAPP_MANUAL_SLOT="yes"
RDEPEND="
dev-libs/openssl:0=
media-libs/libpng:0=
!<sci-biology/ucsc-genome-browser-223
mysql? ( dev-db/mysql-connector-c:0= )
server? ( virtual/httpd-cgi )" # TODO: test with other webservers
DEPEND="${RDEPEND} app-arch/unzip"
S="${WORKDIR}/kent"
src_prepare() {
default
use server && webapp_src_preinst
# bug #708064
append-flags -fcommon
sed \
-e 's/-Werror//' \
-e "/COPT/s:=.*$:=${LDFLAGS}:g" \
-e "s/CC=gcc/CC=$(tc-getCC) ${CFLAGS}/" \
-e 's:${CC} ${COPT} ${CFLAGS}:${CC} ${CFLAGS}:g' \
-i src/inc/common.mk src/hg/lib/makefile || die
find -name makefile -or -name cgi_build_rules.mk \
| xargs sed -i \
-e 's/-${USER}//g' \
-e 's/-$(USER)//g' \
-e 's:-O2::g' \
-e 's:-ggdb::g' \
-e 's:-pipe::g' || die
sed \
-e 's:${DISTDIR}${BINDIR}:${BINDIR}:g' \
-i src/hg/genePredToMafFrames/makefile || 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}:${PATH}" \
STRIP="echo 'skipping strip' "
export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none"
use mysql && export MYSQLLIBS="-L${EROOT}usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \
MYSQLINC="${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" "$DOCUMENTROOT"
emake -C src clean
emake -C src/lib
emake -C src/jkOwnLib
emake -C src/utils/stringify
emake -C src blatSuite
if use mysql; then
emake -j1 -C src/hg utils
emake -j1 -C src utils
emake -C src libs userApps
if use server; then
emake -j1 -C src/hg
emake -j1 -C src
fi
fi
}
src_install() {
use server && webapp_src_preinst
cp -ad "${WORKDIR}"/destdir/* "${D}" || die
use static-libs && dolib.a src/lib/${MACHTYPE/-*/}/*.a
echo "PATH=${EPREFIX}/opt/${PN}/bin" > "${S}/98${PN}"
doenvd "${S}/98${PN}"
use server && webapp_postinst_txt en src/product/README.QuickStart
use server && webapp_src_install
insinto "/usr/include/${PN}"
doins src/inc/*.h
insinto "/usr/share/${PN}"
doins -r src/product
keepdir "/usr/share/doc/${PF}"
find -name 'README*' -or -name '*.doc' | grep -v test | cpio -padv "${ED}/usr/share/doc/${PF}" || die
}
pkg_postinst() {
use server && webapp_pkg_postinst
}
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