1 files changed, 123 insertions, 0 deletions
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild
new file mode 100644
index 000000000000..ef96f491fb51
--- /dev/null
+++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild
@@ -0,0 +1,123 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+WEBAPP_MANUAL_SLOT="yes"
+# TODO: use WEBAPP_OPTIONAL?
+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${PV}.zip"
+S="${WORKDIR}/kent"
+
+LICENSE="blat"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+mysql +server static-libs"
+REQUIRED_USE="server? ( mysql )"
+
+# TODO: test with other webservers
+RDEPEND="
+	dev-libs/openssl:=
+	media-libs/libpng:=
+	!<sci-biology/ucsc-genome-browser-223
+	mysql? ( dev-db/mysql-connector-c:= )
+	server? ( virtual/httpd-cgi )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	app-alternatives/cpio
+	app-arch/unzip
+"
+
+pkg_setup() {
+	use server && webapp_pkg_setup
+}
+
+src_prepare() {
+	default
+
+	use server && webapp_src_preinst
+
+	# bug #708064
+	append-flags -fcommon
+	# bug #831491, bug #919200, bug #921261
+	append-flags -std=gnu89
+
+	sed \
+		-e 's/-Werror//' \
+		-e "/COPT/s:=.*$:=${LDFLAGS}:g" \
+		-e "s/CC=gcc/CC=$(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}:${PATH}" \
+		STRIP="echo 'skipping strip' "
+
+	export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none"
+
+	# TODO: use pkg-config here
+	use mysql && export MYSQLLIBS="-L${ESYSROOT}/usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \
+		MYSQLINC="${ESYSROOT}/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
+}