Import from Science overlay

(Portage version: 2.2_rc30/cvs/Linux x86_64)

3 files changed, 115 insertions, 0 deletions

diff --git a/sci-biology/ucsc-genome-browser/ChangeLog b/sci-biology/ucsc-genome-browser/ChangeLog
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+++ b/sci-biology/ucsc-genome-browser/ChangeLog
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+# ChangeLog for sci-biology/ucsc-genome-browser
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ucsc-genome-browser/ChangeLog,v 1.1 2009/10/28 20:47:27 weaver Exp $
+
+*ucsc-genome-browser-217 (28 Oct 2009)
+
+  28 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml,
+  +ucsc-genome-browser-217.ebuild:
+  Import from Science overlay
+
+  23 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
+  New package, bug 155780. Ebuild written by me and dawe <daweonline@gmail.com>
+
diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml
new file mode 100644
index 000000000000..d66388d73b36
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+++ b/sci-biology/ucsc-genome-browser/metadata.xml
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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<herd>sci-biology</herd>
+	<use>
+		<flag name='server'>Install genome browser Web application. If this flag is off, only libraries and utilities from the suite are installed.</flag>
+	</use>
+</pkgmetadata>
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-217.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-217.ebuild
new file mode 100644
index 000000000000..ef73f7d37aa0
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+++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-217.ebuild
@@ -0,0 +1,90 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ucsc-genome-browser/ucsc-genome-browser-217.ebuild,v 1.1 2009/10/28 20:47:27 weaver Exp $
+
+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${PV}.zip"
+
+LICENSE="blat"
+# webapp ebuilds do not set SLOT
+KEYWORDS="~amd64 ~x86"
+IUSE="+mysql +server"
+
+DEPEND="app-arch/unzip
+	mysql? ( virtual/mysql )
+	server? ( virtual/httpd-cgi )" # TODO: test with other webservers
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/kent"
+
+src_prepare() {
+	if use server && ! use mysql; then die "USE flag server requires USE flag mysql"; fi
+	use server && webapp_src_preinst
+	sed -i -e 's/-Werror//' \
+		-e "s/CC=gcc/CC=$(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" "$DOCUMENTROOT"
+
+	emake -C src clean || die
+	emake -C src/lib || die
+	emake -C src/jkOwnLib || die
+	emake -C src/utils/stringify || die
+	emake -C src blatSuite || die
+	if use mysql; then
+		emake -j1 -C src/hg utils || die
+		emake -j1 -C src utils || die
+		emake -C src libs userApps || die
+		if use server; then
+			emake -j1 -C src/hg || die
+			emake -j1 -C src || die
+		fi
+	fi
+}
+
+src_install() {
+	use server && webapp_src_preinst
+	cp -a "${WORKDIR}"/destdir/* "${D}" || die
+	dolib.a src/lib/${MACHTYPE/-*/}/*.a || die
+	echo "PATH=/opt/${PN}/bin" > "${S}/99${PN}"
+	doenvd "${S}/99${PN}"
+
+	use server && webapp_postinst_txt en src/product/README.QuickStart
+	use server && webapp_src_install
+
+	insinto "/usr/include/${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 "${D}/usr/share/doc/${PF}" || die
+}
+
+pkg_postinst() {
+	use server && webapp_pkg_postinst
+}