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author | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 13:49:04 -0700 |
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committer | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 17:38:18 -0700 |
commit | 56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch) | |
tree | 3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-biology/ucsc-genome-browser | |
download | gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2 gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip |
proj/gentoo: Initial commit
This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.
This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.
Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-biology/ucsc-genome-browser')
-rw-r--r-- | sci-biology/ucsc-genome-browser/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/ucsc-genome-browser/metadata.xml | 8 | ||||
-rw-r--r-- | sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild | 106 |
3 files changed, 115 insertions, 0 deletions
diff --git a/sci-biology/ucsc-genome-browser/Manifest b/sci-biology/ucsc-genome-browser/Manifest new file mode 100644 index 000000000000..3cf6c6051f97 --- /dev/null +++ b/sci-biology/ucsc-genome-browser/Manifest @@ -0,0 +1 @@ +DIST jksrc.v260.zip 59090224 SHA256 ec28dad706f69a02f8d8fb56b9e3010f5e23b7880d717e58d9bb8d1e258fe7d1 SHA512 48aa964ab3ae456ab7e7ddc5d73b91774bd4892f21f1498578a5de38d3a07e4684778ddb1ac1ae389d5bbb3586f9b8506ca3697acca1f6777b85d343cf5d9485 WHIRLPOOL 669b0f342a97f84164b32707a3b2bb51f64219168beceb8f9d46211749351b2c65b21ffe830f82620e7112a332e88ca271d4327739d8f93afbe14e399e45e248 diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml new file mode 100644 index 000000000000..f1f3ccfb77e0 --- /dev/null +++ b/sci-biology/ucsc-genome-browser/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <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 new file mode 100644 index 000000000000..d897ce479df7 --- /dev/null +++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild @@ -0,0 +1,106 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +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 +} |