Version Bump, move to EAPI=4, handled static-libs, respect mostly everywhere LDFALGS

Package-Manager: portage-2.2.0_alpha83/cvs/Linux x86_64

4 files changed, 130 insertions, 5 deletions

diff --git a/sci-biology/ucsc-genome-browser/ChangeLog b/sci-biology/ucsc-genome-browser/ChangeLog
index b0ea7532d514..09eba0f0864f 100644
--- a/sci-biology/ucsc-genome-browser/ChangeLog
+++ b/sci-biology/ucsc-genome-browser/ChangeLog
@@ -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@gentoo.org> +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@gentoo.org>
   ucsc-genome-browser-223.ebuild:
diff --git a/sci-biology/ucsc-genome-browser/Manifest b/sci-biology/ucsc-genome-browser/Manifest
index 229ebc76889b..23f63c59e381 100644
--- a/sci-biology/ucsc-genome-browser/Manifest
+++ b/sci-biology/ucsc-genome-browser/Manifest
@@ -1,4 +1,16 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
 DIST jksrc.v223.zip 121052301 RMD160 ded5f3498d10321bc429b2513226951ddc1b6de8 SHA1 19983219b6b37a40669b8a4b59fab148ed0e0398 SHA256 07d1a638469e7b278aef4e7bda9d8d3c0bb200003f9e866c4bef5d52f7ad75c9
+DIST jksrc.v260.zip 59090224 RMD160 2669795d4cb07b05d75aef9dedc4d9a415f1152a SHA1 933e8649923fa4b2f6cce91f063b9f5c38d05464 SHA256 ec28dad706f69a02f8d8fb56b9e3010f5e23b7880d717e58d9bb8d1e258fe7d1
 EBUILD ucsc-genome-browser-223.ebuild 2848 RMD160 21115ee2bb331d1d4d10933016b682fe21806a88 SHA1 25be7d6f335cb4319268a63eb604f1d2bf8e52b2 SHA256 2ee89fd5991244142b46bbe0720fe2166308443769f451642f7e9036d9983a2e
-MISC ChangeLog 1043 RMD160 6de26a3a15da65ee75dc22796b458dab28386d06 SHA1 96125c6376992d4526351724dc3527ca30f2dcce SHA256 4903a2b161bd428d1869463c74a08b863f702ce0e384bf0bfeb71f474d44fa78
-MISC metadata.xml 423 RMD160 f18dba450536d611049bba524f750a75dfa648a1 SHA1 581c198c487ee42b8b52ae84f88244504a4b98e2 SHA256 cc1353022fb93c0a852d690cb5ee1ca8f90496a386e6ff4c6e8eb534f5652658
+EBUILD ucsc-genome-browser-260.ebuild 3055 RMD160 14ac747459a5b87791405279b8b9e3ebe71d57ad SHA1 8c10040a30566d4fd6639f71f4aa1d52d415600b SHA256 8c00967843adf0b4251750c5be0b88a76633169b7ff90a9d4d917edd771b77d0
+MISC ChangeLog 1267 RMD160 bb94f25f456846c59c9773efb40f415d43904888 SHA1 b470e483c4d892932f95ed198b4e8fedd201bc8f SHA256 c4657ad4692480207e9c068f1ec0d8777d21d1cd864b2b0af072f48838431574
+MISC metadata.xml 423 RMD160 6a9d4d65091ecd4ec4881a38eeefbe893905864f SHA1 7528729d1ccfd166bb41fcf0a9782a5cb9ead060 SHA256 7701d1497e436dcc46584b6832287089150e8ece50c1dc21cdbe30f12731c332
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.18 (GNU/Linux)
+
+iEYEAREKAAYFAk75kkIACgkQgAnW8HDreRYdDwCfUca1DUPVo4sHoq7EHl3+2NZP
+0pgAoIHfmFGtHquB3wTwRsFs6KHzCmKE
+=Xqtg
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml
index d66388d73b36..18137f66a1d5 100644
--- a/sci-biology/ucsc-genome-browser/metadata.xml
+++ b/sci-biology/ucsc-genome-browser/metadata.xml
@@ -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>
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild
new file mode 100644
index 000000000000..06a796499aee
--- /dev/null
+++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild
@@ -0,0 +1,106 @@
+# 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
+}