From 79599515788b85b18aa655e7b7f8cc05c1bbddd8 Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@redcorelinux.org>
Date: Sat, 16 Feb 2019 12:59:29 +0000
Subject: gentoo resync : 16.02.1018

---
 sci-biology/Manifest.gz                            | Bin 25306 -> 25300 bytes
 sci-biology/ucsc-genome-browser/Manifest           |   2 +-
 .../ucsc-genome-browser-260-r1.ebuild              | 107 +++++++++++++++++++++
 .../ucsc-genome-browser-260.ebuild                 | 105 --------------------
 4 files changed, 108 insertions(+), 106 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/Manifest.gz b/sci-biology/Manifest.gz
index dfe16f3674cb..10d9f9b7fe27 100644
Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ
diff --git a/sci-biology/ucsc-genome-browser/Manifest b/sci-biology/ucsc-genome-browser/Manifest
index a45d2f241ce4..9e79c09fcb4d 100644
--- a/sci-biology/ucsc-genome-browser/Manifest
+++ b/sci-biology/ucsc-genome-browser/Manifest
@@ -1,3 +1,3 @@
 DIST jksrc.v260.zip 59090224 BLAKE2B 755bb97f50cde97e7634f38aa81f0843de52710cac78f5b0a2ee6129cffc99f730b8e1ab41d24e2faebb3c0a3e1d1309c84307e2dc4af1efe9a30fb0b9ae1670 SHA512 48aa964ab3ae456ab7e7ddc5d73b91774bd4892f21f1498578a5de38d3a07e4684778ddb1ac1ae389d5bbb3586f9b8506ca3697acca1f6777b85d343cf5d9485
-EBUILD ucsc-genome-browser-260.ebuild 2920 BLAKE2B c58ea503f59176f8a2a08851bc99658aff03f8375778a8e53a1c3840601fee7f63e4f39711aee4e5adcbe433192f2bfcf5a8c2a429a0b9d87f48bd63ac2ae3c3 SHA512 4b9f58349249201f35454c99a1e1e35f3aa5bd4a1477fb534b8843bec52212768859b85c0e14aece50a02b2920c297ed96717d13a111583ed023f59b00481f7a
+EBUILD ucsc-genome-browser-260-r1.ebuild 2983 BLAKE2B f55b32bfa34dca32798f2ba99c1c80acb7ed8bb5b91ae284d34a1ce371dfe7b1f2c06169ffc3a19ad423ac0deffe764b0dd132323099ccd6f12a505e3a37071c SHA512 725bd144ae33ba872508218b7e63d9147e1edbf8748dbe3a05cb0757cbb96fd6ea31c0e64b303f30738fb770e04a7bfb6df50d96c217d71fd7a68591dded31d5
 MISC metadata.xml 435 BLAKE2B fb242aaf17920e320c65bbd8bf83c79ffc0a9e97c112e2e19f89ed9c0a3fd2e48e7444c81dd82bc30b38c1e9251737d93bea310f77ddff5a183301276588b1a3 SHA512 1acffee210c77abc41a93b5b78e52b27ed18df50a2eff3c6463e34bc031a4b2c97d1472a0dcf14bbf513c77d930a67434194c2e5ac435a5f7fd1e79294335a81
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
-}
-- 
cgit v1.2.3