From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@redcorelinux.org>
Date: Mon, 9 Oct 2017 18:53:29 +0100
Subject: reinit the tree, so we can have metadata

---
 sci-biology/ucsc-genome-browser/Manifest           |   5 +
 sci-biology/ucsc-genome-browser/metadata.xml       |  11 +++
 .../ucsc-genome-browser-260.ebuild                 | 105 +++++++++++++++++++++
 3 files changed, 121 insertions(+)
 create mode 100644 sci-biology/ucsc-genome-browser/Manifest
 create mode 100644 sci-biology/ucsc-genome-browser/metadata.xml
 create mode 100644 sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild

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

diff --git a/sci-biology/ucsc-genome-browser/Manifest b/sci-biology/ucsc-genome-browser/Manifest
new file mode 100644
index 000000000000..9b21e29f6f4b
--- /dev/null
+++ b/sci-biology/ucsc-genome-browser/Manifest
@@ -0,0 +1,5 @@
+DIST jksrc.v260.zip 59090224 SHA256 ec28dad706f69a02f8d8fb56b9e3010f5e23b7880d717e58d9bb8d1e258fe7d1 SHA512 48aa964ab3ae456ab7e7ddc5d73b91774bd4892f21f1498578a5de38d3a07e4684778ddb1ac1ae389d5bbb3586f9b8506ca3697acca1f6777b85d343cf5d9485 WHIRLPOOL 669b0f342a97f84164b32707a3b2bb51f64219168beceb8f9d46211749351b2c65b21ffe830f82620e7112a332e88ca271d4327739d8f93afbe14e399e45e248
+EBUILD ucsc-genome-browser-260.ebuild 2920 SHA256 d88b2c78291cc64137193b4a300aae814b488721f6326f78c53f84948730b2e1 SHA512 4b9f58349249201f35454c99a1e1e35f3aa5bd4a1477fb534b8843bec52212768859b85c0e14aece50a02b2920c297ed96717d13a111583ed023f59b00481f7a WHIRLPOOL 92e470312ad45d04fbb09a780b72aec6b591e84b3b66c85b0c7716f4edfbfc823fd8a2500167ee4ab10d4e7dd4d1c877337aed2f2d876af9c1bb3843f8cce65c
+MISC ChangeLog 2462 SHA256 f0197213b438d3f1ddd7a9c8933f488201638602b1b81edf833ef7c3374e3a92 SHA512 0bf627625bb844f013b3f15ee03bd151ea482e641def0a606f35c097763b7ee3bc95fd33d859921cc31b36b015f61282459bedbe8da487f361b5103ff985b426 WHIRLPOOL e22226d2842233abfaa4abcc7e6c937600cd77dd05a9fa85992360047b03736b73c67eff24fd8a04ae7272193421427ab5efad59a21deaa680bffac2f488d36a
+MISC ChangeLog-2015 1543 SHA256 e4528cb56770a7989b4c681b2ca915691d1c4efde053d96bb152ed077ec5bbf8 SHA512 e4f17c85b1df30b7277271edc19409cd9062a64704023ff975ef51321428e3bdae035f1f5f487ebadfa1eef4fc6e3cae2aa788d57b68c27875e88465e7f1c6fc WHIRLPOOL fd8bceba956dd2506377ba6748f43a4fbbb753b35e7bd2397b0955a840b32b20a643d5f4498d2f05acc71094e51523f29f08c3b6e129eb9712fc7ac1791014eb
+MISC metadata.xml 435 SHA256 937efe8e0861e55f1d8d4aa0d431e262657c10e3476041113f6561aee3290a59 SHA512 1acffee210c77abc41a93b5b78e52b27ed18df50a2eff3c6463e34bc031a4b2c97d1472a0dcf14bbf513c77d930a67434194c2e5ac435a5f7fd1e79294335a81 WHIRLPOOL 7601aae3dd7ebbc856edc983a0b2a38fe8687c52af40065fea816e09778be45311182468a72fd9078489ca49634d2e41263ada07b088ea626b577bb95bdaba31
diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml
new file mode 100644
index 000000000000..042f7b949ba9
--- /dev/null
+++ b/sci-biology/ucsc-genome-browser/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <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
new file mode 100644
index 000000000000..7ce025b2ae95
--- /dev/null
+++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild
@@ -0,0 +1,105 @@
+# 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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