commit: 06204e7a240e106b481983bdaf48fc4aa9719a4c Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Jan 7 22:27:12 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Jan 7 22:27:12 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=06204e7a
bioperl/bioperl-1.6.901: dropped an ebuild with USE=+static, otherwise same in main tree --- sci-biology/bioperl/bioperl-1.6.901.ebuild | 81 ++++++++++++++++ sci-biology/bioperl/metadata.xml | 5 + sci-biology/ucsc-genome-browser/metadata.xml | 12 +++ .../ucsc-genome-browser-260.ebuild | 106 +++++++++++++++++++++ 4 files changed, 204 insertions(+) diff --git a/sci-biology/bioperl/bioperl-1.6.901.ebuild b/sci-biology/bioperl/bioperl-1.6.901.ebuild new file mode 100644 index 0000000..98d0763 --- /dev/null +++ b/sci-biology/bioperl/bioperl-1.6.901.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.6.1.ebuild,v 1.3 2009/10/02 14:51:51 weaver Exp $ + +EAPI="2" + +inherit perl-module + +SUBPROJECTS="+db +network +run" +MIN_PV="1.6" + +DESCRIPTION="Perl tools for bioinformatics - Core modules" +HOMEPAGE="http://www.bioperl.org/"; +# SRC_URI="http://www.bioperl.org/DIST/BioPerl-${PV}.tar.bz2"; +SRC_URI="http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-${PV}.tar.gz"; + +LICENSE="Artistic GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="-minimal graphviz sqlite ${SUBPROJECTS}" + +CDEPEND=">=perl-core/Module-Build-0.380.0 + dev-perl/Data-Stag + dev-perl/libwww-perl + !minimal? ( + dev-perl/Ace + dev-perl/Spreadsheet-ParseExcel + dev-perl/Spreadsheet-WriteExcel + >=dev-perl/XML-SAX-0.15 + dev-perl/Graph + dev-perl/SOAP-Lite + dev-perl/Array-Compare + dev-perl/SVG + dev-perl/XML-Simple + dev-perl/XML-Parser + dev-perl/XML-Twig + >=dev-perl/HTML-Parser-3.60 + >=dev-perl/XML-Writer-0.4 + dev-perl/Clone + dev-perl/XML-DOM + dev-perl/set-scalar + dev-perl/XML-XPath + dev-perl/XML-DOM-XPath + dev-perl/Algorithm-Munkres + dev-perl/Data-Stag + dev-perl/Math-Random + dev-perl/PostScript + dev-perl/Convert-Binary-C + dev-perl/SVG-Graph + dev-perl/IO-String + dev-perl/Class-Inspector + dev-perl/Sort-Naturally + ) + graphviz? ( dev-perl/GraphViz ) + sqlite? ( dev-perl/DBD-SQLite )" +DEPEND="virtual/perl-Module-Build + ${CDEPEND}" +# In perl-overlay +# >=virtual/perl-ExtUtils-Manifest-1.52 (to CDEPEND?) +# >=perl-CPAN/perl-CPAN-1.81 +RDEPEND="${CDEPEND}" +PDEPEND="!minimal? ( dev-perl/Bio-ASN1-EntrezGene ) + db? ( >=sci-biology/bioperl-db-${MIN_PV} ) + network? ( >=sci-biology/bioperl-network-${MIN_PV} ) + run? ( >=sci-biology/bioperl-run-${MIN_PV} )" + +S="${WORKDIR}/BioPerl-${PV}" + +src_configure() { + sed -i -e '/add_post_install_script.*symlink_script.pl/d' \ + -e "/'CPAN' *=> *1.81/d" \ + -e "/'ExtUtils::Manifest' *=> *'1.52'/d" "${S}/Build.PL" || die + + if use minimal && use graphviz; then die "USE flags minimal and graphviz cannot be used together"; fi + perl-module_src_configure +} + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml new file mode 100644 index 0000000..d464821 --- /dev/null +++ b/sci-biology/bioperl/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml new file mode 100644 index 0000000..18137f6 --- /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>[email protected]</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-260.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild new file mode 100644 index 0000000..ae00dd8 --- /dev/null +++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild @@ -0,0 +1,106 @@ +# Copyright 1999-2011 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-260.ebuild,v 1.1 2011/12/27 09:39:04 jlec Exp $ + +EAPI=4 + +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 +}
