From 3a0588753c86399d7c514bc34d22f48687cbcbfe Mon Sep 17 00:00:00 2001
From: Brian Evans <grknight@gentoo.org>
Date: Fri, 15 Feb 2019 16:09:14 -0500
Subject: sci-biology/ucsc-genome-browser: Revbump to fix dependencies

Non-maintainer commit

Closes: https://bugs.gentoo.org/667578
Closes: https://bugs.gentoo.org/666050
Package-Manager: Portage-2.3.60, Repoman-2.3.12
Signed-off-by: Brian Evans <grknight@gentoo.org>
---
 .../ucsc-genome-browser-260-r1.ebuild              | 107 +++++++++++++++++++++
 .../ucsc-genome-browser-260.ebuild                 | 105 --------------------
 2 files changed, 107 insertions(+), 105 deletions(-)
 create mode 100644 sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
 delete mode 100644 sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild

(limited to 'sci-biology')

diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
new file mode 100644
index 000000000000..9b53170b1e83
--- /dev/null
+++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
@@ -0,0 +1,107 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+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${PV}.zip"
+
+LICENSE="blat"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+mysql +server static-libs"
+
+REQUIRED_USE="server? ( mysql )"
+
+WEBAPP_MANUAL_SLOT="yes"
+
+RDEPEND="
+	dev-libs/openssl:0=
+	media-libs/libpng:0=
+	!<sci-biology/ucsc-genome-browser-223
+	mysql? ( dev-db/mysql-connector-c:0= )
+	server? ( virtual/httpd-cgi )" # TODO: test with other webservers
+DEPEND="${RDEPEND} app-arch/unzip"
+
+S="${WORKDIR}/kent"
+
+src_prepare() {
+	default
+	use server && webapp_src_preinst
+	sed \
+		-e 's/-Werror//' \
+		-e "/COPT/s:=.*$:=${LDFLAGS}:g" \
+		-e "s/CC=gcc/CC=$(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/${PF}" || die
+}
+
+pkg_postinst() {
+	use server && webapp_pkg_postinst
+}
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild
deleted file mode 100644
index 7ce025b2ae95..000000000000
--- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild
+++ /dev/null
@@ -1,105 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs flag-o-matic webapp
-
-DESCRIPTION="The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath"
-HOMEPAGE="http://genome.ucsc.edu/"
-SRC_URI="http://hgdownload.cse.ucsc.edu/admin/jksrc.v${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
-}
-- 
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