diff options
| -rw-r--r-- | sci-biology/ucsc-genome-browser/ChangeLog | 13 | ||||
| -rw-r--r-- | sci-biology/ucsc-genome-browser/Manifest | 4 | ||||
| -rw-r--r-- | sci-biology/ucsc-genome-browser/metadata.xml | 12 | ||||
| -rw-r--r-- | sci-biology/ucsc-genome-browser/ucsc-genome-browser-217.ebuild | 90 |
4 files changed, 119 insertions, 0 deletions
diff --git a/sci-biology/ucsc-genome-browser/ChangeLog b/sci-biology/ucsc-genome-browser/ChangeLog new file mode 100644 index 000000000000..238c42c7a84a --- /dev/null +++ b/sci-biology/ucsc-genome-browser/ChangeLog @@ -0,0 +1,13 @@ +# ChangeLog for sci-biology/ucsc-genome-browser +# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ucsc-genome-browser/ChangeLog,v 1.1 2009/10/28 20:47:27 weaver Exp $ + +*ucsc-genome-browser-217 (28 Oct 2009) + + 28 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +ucsc-genome-browser-217.ebuild: + Import from Science overlay + + 23 Oct 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: + New package, bug 155780. Ebuild written by me and dawe <daweonline@gmail.com> + diff --git a/sci-biology/ucsc-genome-browser/Manifest b/sci-biology/ucsc-genome-browser/Manifest new file mode 100644 index 000000000000..3c89a3b3f8dc --- /dev/null +++ b/sci-biology/ucsc-genome-browser/Manifest @@ -0,0 +1,4 @@ +DIST jksrc.v217.zip 118362449 RMD160 65ca4e0caefaf42cdf7885e55063216fd69fd8f2 SHA1 3df81e7dfd4fd56a6afac69590f9ecb53e9174c5 SHA256 53e95bfcc68644cc20e0d3707161044b0d231c94199e4b0702b91ae72db21c20 +EBUILD ucsc-genome-browser-217.ebuild 2808 RMD160 05aa1c385194400a7677edb697451c6a5d52719a SHA1 6eb6bd5244a452d1cc972d47045d0b2505129d6c SHA256 ced5c77652f5501cc1ab38f9f698eeb9fe1d8728cbfc3f335c2dc9c3c2ca4398 +MISC ChangeLog 548 RMD160 871960dfe4780e981837443b49810de557e82e0b SHA1 973ed1d928f7b261b09003ddb76f45f2a15779c3 SHA256 15e6bbd8268cd9d73c17c676c41a2926275ad563868f60c9dc23f158edb8269f +MISC metadata.xml 423 RMD160 f18dba450536d611049bba524f750a75dfa648a1 SHA1 581c198c487ee42b8b52ae84f88244504a4b98e2 SHA256 cc1353022fb93c0a852d690cb5ee1ca8f90496a386e6ff4c6e8eb534f5652658 diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml new file mode 100644 index 000000000000..d66388d73b36 --- /dev/null +++ b/sci-biology/ucsc-genome-browser/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>weaver@gentoo.org</email> + <name>Andrey Kislyuk</name> + </maintainer> + <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-217.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-217.ebuild new file mode 100644 index 000000000000..ef73f7d37aa0 --- /dev/null +++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-217.ebuild @@ -0,0 +1,90 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ucsc-genome-browser/ucsc-genome-browser-217.ebuild,v 1.1 2009/10/28 20:47:27 weaver Exp $ + +EAPI="2" + +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${PV}.zip" + +LICENSE="blat" +# webapp ebuilds do not set SLOT +KEYWORDS="~amd64 ~x86" +IUSE="+mysql +server" + +DEPEND="app-arch/unzip + mysql? ( virtual/mysql ) + server? ( virtual/httpd-cgi )" # TODO: test with other webservers +RDEPEND="${DEPEND}" + +S="${WORKDIR}/kent" + +src_prepare() { + if use server && ! use mysql; then die "USE flag server requires USE flag mysql"; fi + use server && webapp_src_preinst + sed -i -e 's/-Werror//' \ + -e "s/CC=gcc/CC=$(tc-getCC) ${CFLAGS}/" \ + src/inc/common.mk || die + find -name makefile -or -name cgi_build_rules.mk \ + | xargs sed -i -e 's/-${USER}//g' -e 's/-$(USER)//g' || die +} + +src_compile() { + export MACHTYPE=${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="${ROOT}usr/lib/mysql/libmysqlclient.a -lz -lssl" \ + MYSQLINC="${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" "$DOCUMENTROOT" + + emake -C src clean || die + emake -C src/lib || die + emake -C src/jkOwnLib || die + emake -C src/utils/stringify || die + emake -C src blatSuite || die + if use mysql; then + emake -j1 -C src/hg utils || die + emake -j1 -C src utils || die + emake -C src libs userApps || die + if use server; then + emake -j1 -C src/hg || die + emake -j1 -C src || die + fi + fi +} + +src_install() { + use server && webapp_src_preinst + cp -a "${WORKDIR}"/destdir/* "${D}" || die + dolib.a src/lib/${MACHTYPE/-*/}/*.a || die + echo "PATH=/opt/${PN}/bin" > "${S}/99${PN}" + doenvd "${S}/99${PN}" + + use server && webapp_postinst_txt en src/product/README.QuickStart + use server && webapp_src_install + + insinto "/usr/include/${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 "${D}/usr/share/doc/${PF}" || die +} + +pkg_postinst() { + use server && webapp_pkg_postinst +} |