[gentoo-commits] gentoo-x86 commit in sci-biology/ucsc-genome-browser: metadata.xml ChangeLog ucsc-genome-browser-260.ebuild

[Justin Lecher (jlec)]

jlec        11/12/27 09:39:04

  Modified:             metadata.xml ChangeLog
  Added:                ucsc-genome-browser-260.ebuild
  Log:
  Version Bump, move to EAPI=4, handled static-libs, respect mostly everywhere LDFALGS
  
  (Portage version: 2.2.0_alpha83/cvs/Linux x86_64)

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

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ucsc-genome-browser/metadata.xml?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ucsc-genome-browser/metadata.xml?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ucsc-genome-browser/metadata.xml?r1=1.1&r2=1.2

Index: metadata.xml
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/ucsc-genome-browser/metadata.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- metadata.xml	28 Oct 2009 20:47:27 -0000	1.1
+++ metadata.xml	27 Dec 2011 09:39:04 -0000	1.2
@@ -7,6 +7,6 @@
 	</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>
+		<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>



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

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ucsc-genome-browser/ChangeLog?rev=1.5&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ucsc-genome-browser/ChangeLog?rev=1.5&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ucsc-genome-browser/ChangeLog?r1=1.4&r2=1.5

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/ucsc-genome-browser/ChangeLog,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- ChangeLog	24 Feb 2010 21:43:32 -0000	1.4
+++ ChangeLog	27 Dec 2011 09:39:04 -0000	1.5
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/ucsc-genome-browser
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ucsc-genome-browser/ChangeLog,v 1.4 2010/02/24 21:43:32 weaver Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ucsc-genome-browser/ChangeLog,v 1.5 2011/12/27 09:39:04 jlec Exp $
+
+*ucsc-genome-browser-260 (27 Dec 2011)
+
+  27 Dec 2011; Justin Lecher <jlec@g.o> +ucsc-genome-browser-260.ebuild,
+  metadata.xml:
+  Version Bump, move to EAPI=4, handled static-libs, respect mostly everywhere
+  LDFALGS
 
   24 Feb 2010; Andrey Kislyuk <weaver@g.o>
   ucsc-genome-browser-223.ebuild:



1.1                  sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild?rev=1.1&content-type=text/plain

Index: ucsc-genome-browser-260.ebuild
===================================================================
# Copyright 1999-2011 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-260.ebuild,v 1.1 2011/12/27 09:39:04 jlec Exp $

EAPI=4

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"

DEPEND="
	app-arch/unzip
	!<sci-biology/ucsc-genome-browser-223
	mysql? ( virtual/mysql )
	server? ( virtual/httpd-cgi )" # TODO: test with other webservers
RDEPEND="${DEPEND}"

S="${WORKDIR}/kent"

src_prepare() {
	use server && webapp_src_preinst
	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
}