[gentoo-commits] proj/sci:master commit in: sci-biology/ucsc-genome-browser/

[gentoo-commits] proj/sci:master commit in: sci-biology/ucsc-genome-browser/

[Justin Lecher]

commit:     877d4bcc7fc3f8f3255757a09f54ca343758c65a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Apr 16 06:28:21 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Apr 16 06:28:21 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=877d4bcc

In CVS

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/ucsc-genome-browser/metadata.xml       |  12 ---
 .../ucsc-genome-browser-260.ebuild                 | 106 ---------------------
 2 files changed, 118 deletions(-)

diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml
deleted file mode 100644
index 18137f6..0000000
--- a/sci-biology/ucsc-genome-browser/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?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-260.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild
deleted file mode 100644
index f81e171..0000000
--- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild
+++ /dev/null
@@ -1,106 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-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
-}