[gentoo-commits] gentoo-x86 commit in sci-biology/ucsc-genome-browser: metadata.xml ucsc-genome-browser-217.ebuild ChangeLog

[Andrey Kislyuk (weaver)]

weaver      09/10/28 20:47:28

  Added:                metadata.xml ucsc-genome-browser-217.ebuild
                        ChangeLog
  Log:
  Import from Science overlay
  (Portage version: 2.2_rc30/cvs/Linux x86_64)

Revision  Changes    Path
1.1                  sci-biology/ucsc-genome-browser/metadata.xml

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/ucsc-genome-browser/metadata.xml?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/ucsc-genome-browser/metadata.xml?rev=1.1&content-type=text/plain

Index: metadata.xml
===================================================================
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
	<maintainer>
		<email>weaver@g.o</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>



1.1                  sci-biology/ucsc-genome-browser/ucsc-genome-browser-217.ebuild

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/ucsc-genome-browser/ucsc-genome-browser-217.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/ucsc-genome-browser/ucsc-genome-browser-217.ebuild?rev=1.1&content-type=text/plain

Index: ucsc-genome-browser-217.ebuild
===================================================================
# 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
}



1.1                  sci-biology/ucsc-genome-browser/ChangeLog

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/ucsc-genome-browser/ChangeLog?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/ucsc-genome-browser/ChangeLog?rev=1.1&content-type=text/plain

Index: ChangeLog
===================================================================
# 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@g.o> +metadata.xml,
  +ucsc-genome-browser-217.ebuild:
  Import from Science overlay

  23 Oct 2009; Andrey Kislyuk <weaver@g.o> ChangeLog:
  New package, bug 155780. Ebuild written by me and dawe <daweonline@×××××.com>