From a3bb28551df94028000fb72308a9e9baa01458b0 Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@koprulu.sector>
Date: Mon, 3 Jun 2024 00:07:26 +0100
Subject: gentoo auto-resync : 03:06:2024 - 00:07:25

---
 sci-biology/ucsc-genome-browser/Manifest           |   2 +-
 .../ucsc-genome-browser-260-r1.ebuild              | 114 -------------------
 .../ucsc-genome-browser-260-r2.ebuild              | 123 +++++++++++++++++++++
 3 files changed, 124 insertions(+), 115 deletions(-)
 delete mode 100644 sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
 create mode 100644 sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild

(limited to 'sci-biology/ucsc-genome-browser')

diff --git a/sci-biology/ucsc-genome-browser/Manifest b/sci-biology/ucsc-genome-browser/Manifest
index 13c0c81fd95e..352d6f97739a 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-r1.ebuild 3134 BLAKE2B f9b628c78939377f66c9aca6b68ca3cbebf7c41dde18a8d03dbc4533593069dff0381d0fe206b0287569739a96010661d275c2d43a8ffc9e1ad8f73b4d73be5e SHA512 6f33bd29ac24661d8a495913b6746d60ca4eb95e91e5ca7325420a9b430f9ca8fe990d9167ab2ffd500f151f8cce045601e1dde24efde05b185511c1b06593a7
+EBUILD ucsc-genome-browser-260-r2.ebuild 3247 BLAKE2B 7f8ece657ec2fa39c623712293009645f247f427149e617287d458a97364bf6070a3bc1c94ef2b447c6751e58b0b98f7996c7a941342ed937d9455a84a1233fb SHA512 99716737f5cb5e03ecc162a97a79e8f3369dea1452819c9dce4ae2ec593953b0c031929c0785b8677506483d6537c59d113888b89b804d9796b767f364bfc5cf
 MISC metadata.xml 436 BLAKE2B f0bf2e08eaadf20a1810abf0e3cd42494197b8fe2593c5f3ee243f58af5676a795009fefbc7f11d2d8e4d42ff9e34790dd7be9999a37839fe6ce780b12714116 SHA512 43d2b6e4519270b495122711c747c906ba64993811a6f4d63af5fc17a6752232dde3717f193432d673e2c183e35fb88421a39077d3d0dad18b712d26c6e64caa
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
deleted file mode 100644
index f0bb0676ae85..000000000000
--- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
+++ /dev/null
@@ -1,114 +0,0 @@
-# Copyright 1999-2021 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="${WORKDIR}/kent"
-
-src_prepare() {
-	default
-
-	use server && webapp_src_preinst
-
-	# bug #708064
-	append-flags -fcommon
-
-	sed \
-		-e 's/-Werror//' \
-		-e "/COPT/s:=.*$:=${LDFLAGS}:g" \
-		-e "s/CC=gcc/CC=$(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"
-
-	# TODO: Change ${EPREFIX} to ${ESYSROOT} in EAPI 7
-	# (and ideally use pkg-config here)
-	use mysql && export MYSQLLIBS="-L${EPREFIX%/}/usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \
-		MYSQLINC="${EPREFIX%/}/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/${PF}" || die
-}
-
-pkg_postinst() {
-	use server && webapp_pkg_postinst
-}
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild
new file mode 100644
index 000000000000..ef96f491fb51
--- /dev/null
+++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r2.ebuild
@@ -0,0 +1,123 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+WEBAPP_MANUAL_SLOT="yes"
+# TODO: use WEBAPP_OPTIONAL?
+inherit toolchain-funcs flag-o-matic webapp
+
+DESCRIPTION="The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath"
+HOMEPAGE="http://genome.ucsc.edu/"
+SRC_URI="http://hgdownload.cse.ucsc.edu/admin/jksrc.v${PV}.zip"
+S="${WORKDIR}/kent"
+
+LICENSE="blat"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="+mysql +server static-libs"
+REQUIRED_USE="server? ( mysql )"
+
+# TODO: test with other webservers
+RDEPEND="
+	dev-libs/openssl:=
+	media-libs/libpng:=
+	!<sci-biology/ucsc-genome-browser-223
+	mysql? ( dev-db/mysql-connector-c:= )
+	server? ( virtual/httpd-cgi )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	app-alternatives/cpio
+	app-arch/unzip
+"
+
+pkg_setup() {
+	use server && webapp_pkg_setup
+}
+
+src_prepare() {
+	default
+
+	use server && webapp_src_preinst
+
+	# bug #708064
+	append-flags -fcommon
+	# bug #831491, bug #919200, bug #921261
+	append-flags -std=gnu89
+
+	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}:${PATH}" \
+		STRIP="echo 'skipping strip' "
+
+	export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none"
+
+	# TODO: use pkg-config here
+	use mysql && export MYSQLLIBS="-L${ESYSROOT}/usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \
+		MYSQLINC="${ESYSROOT}/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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