New package, bug 155780. Ebuild written by me and dawe <daweonline@gmail.com>

4 files changed, 102 insertions, 0 deletions

diff --git a/sci-biology/ucsc-genome-browser/ChangeLog b/sci-biology/ucsc-genome-browser/ChangeLog
new file mode 100644
index 000000000..aca31855f
--- /dev/null
+++ b/sci-biology/ucsc-genome-browser/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/ucsc-genome-browser
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  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/Manifest b/sci-biology/ucsc-genome-browser/Manifest
new file mode 100644
index 000000000..b1dc21896
--- /dev/null
+++ b/sci-biology/ucsc-genome-browser/Manifest
@@ -0,0 +1,4 @@
+DIST jksrc.v217.zip 118362449 RMD160 65ca4e0caefaf42cdf7885e55063216fd69fd8f2 SHA1 3df81e7dfd4fd56a6afac69590f9ecb53e9174c5 SHA256 53e95bfcc68644cc20e0d3707161044b0d231c94199e4b0702b91ae72db21c20
+EBUILD ucsc-genome-browser-217.ebuild 2607 RMD160 67bc746b50ead463ddc0189f07f4925677397626 SHA1 55fea7e60b0d3654ee17f8c1dd6d1840d65d0033 SHA256 0e88227f4cbd3567139296bce9109b23f45a05e5debcd9602bab8d525b5cede7
+MISC ChangeLog 241 RMD160 de41ed648a1687c46174e65ebe8c7266b9fc061e SHA1 552b3b62cc5d26c338c7cc7b89de3a26cf89dc35 SHA256 9152a439f65d499788107cf6d770692e1a270a4100bcf7a866a545bc2f4fbcb2
+MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml
new file mode 100644
index 000000000..3302123e5
--- /dev/null
+++ b/sci-biology/ucsc-genome-browser/metadata.xml
@@ -0,0 +1,9 @@
+<?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>
+</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 000000000..9e7b4b803
--- /dev/null
+++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-217.ebuild
@@ -0,0 +1,82 @@
+# 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
+}