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Diffstat (limited to 'sci-biology/gbrowse/gbrowse-2.26.ebuild')
-rw-r--r-- | sci-biology/gbrowse/gbrowse-2.26.ebuild | 147 |
1 files changed, 147 insertions, 0 deletions
diff --git a/sci-biology/gbrowse/gbrowse-2.26.ebuild b/sci-biology/gbrowse/gbrowse-2.26.ebuild new file mode 100644 index 000000000..b525bcca3 --- /dev/null +++ b/sci-biology/gbrowse/gbrowse-2.26.ebuild @@ -0,0 +1,147 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ +EAPI="2" + +inherit perl-module webapp + +MY_P="GBrowse-${PV}" + +DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages" +HOMEPAGE="http://gmod.org" +SRC_URI="mirror://sourceforge/gmod/${MY_P}.tar.gz + test? ( http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2 + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )" + +LICENSE="Artistic" +# webapp ebuilds do not set SLOT +KEYWORDS="~x86 ~amd64" +IUSE="-minimal svg test" # lwp moby scf + +S="${WORKDIR}/${MY_P}" + +# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10) +# TODO: make sure www-servers/apache +cgi +DEPEND=">=dev-lang/perl-5.8.8 + dev-perl/Capture-Tiny + >=sci-biology/bioperl-1.6 + >=dev-perl/GD-2.07 + dev-perl/IO-String + virtual/perl-Digest-MD5 + >=dev-perl/CGI-Session-4.03 + dev-perl/Statistics-Descriptive + >=dev-perl/Bio-Graphics-1.97 + dev-perl/JSON + dev-perl/libwww-perl + svg? ( dev-perl/GD-SVG )" + +# TODO: based on the following message in apache/error_log the list of deps should be longer +# GBROWSE NOTICE: To enable PDF generation, please enter the directory "/home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache .inkscape .gnome2". To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?ref=chrII;start=90739;end=92028;name=YBL069W;class=Sequence;feature_id=881;db_id=annotations%3Adatabase + +# * Bio::DB::BigFile is not installed +# * Bio::DB::Sam is not installed +# * DBD::Pg is not installed + + +RDEPEND="${DEPEND} + >=www-servers/apache-2.0.47 + www-apache/mod_fastcgi + dev-perl/DBI + || ( dev-perl/DBD-Pg dev-perl/DBD-mysql ) + !minimal? ( + dev-perl/File-NFSLock + dev-perl/FCGI + perl-core/Math-BigInt + perl-core/Math-BigInt-FastCalc + dev-perl/Math-BigInt-GMP + dev-perl/Digest-SHA1 + dev-perl/Crypt-SSLeay + dev-perl/Net-SMTP-SSL + dev-perl/Net-OpenID-Consumer + virtual/perl-DB_File + dev-perl/DB_File-Lock + dev-perl/GD-SVG + dev-perl/Text-Shellwords + dev-perl/XML-Twig + dev-perl/XML-DOM + dev-perl/XML-Writer + dev-perl/XML-Parser + dev-perl/Bio-Das + dev-perl/Text-Shellwords + )" + +src_prepare() { + sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die + sed -i 's/process_/bp_process_/g' INSTALL || die + epatch "${FILESDIR}"/GBrowseInstall.pm.patch || die "Failed to patch" +} + +src_configure() { + # GBROWSE_ROOT is the root path in SRC_URI to be prepended + # /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf + webapp_src_preinst + perl Makefile.PL \ + HTDOCS="${MY_HTDOCSDIR}" \ + CGIBIN="${MY_HTDOCSDIR}"/cgi-bin \ + CONF="${MY_HTDOCSDIR}"/etc/gbrowse \ + PACKAGE_DIR="${D}" \ + INSTALLDIRS=vendor \ + GBROWSE_ROOT="gbrowse" \ + DESTDIR="${D}" \ + DATABASES="/var/www/gbrowse2/databases/" \ + TMP="/var/tmp/gbrowse2" \ + INSTALLETC="n" \ + INSTALLCONF="n" \ + WWWUSER="apache" \ + DO_XS=1 \ + NONROOT=1 \ + || die +} + +src_install() { + mydoc="Changes README TODO INSTALL" + perl-module_src_install + + # TODO: write our own readme + webapp_postinst_txt en "${S}"/INSTALL + webapp_src_install || die "Failed running webapp_src_install" + + # should create a /etc/init.d/ startup script based on this + # /var/tmp/portage/sci-biology/gbrowse-2.03/work/GBrowse-2.03/etc/init.d/gbrowse-slave + + chown -R apache.apache "${D}"/var/www/gbrowse2/databases || die + + mkdir -p "${D}"/var/www/localhost/htdocs/gbrowse || die + ln -s "${D}"/var/tmp/gbrowse2/images "${D}"/var/www/localhost/htdocs/gbrowse/i || die + + einfo "Probably you want to install a cron job to remove the generated temporary images:" + einfo "find /var/tmp/gbrowse2/images -type f -atime +20 -print -exec rm {}" + + einfo "Make sure you compiled apache with +cgi and copy ${FILESDIR}/gbrowse.conf.vhosts.d to /etc/apache2/vhosts.d/" +} + +pkg_postinst() { + webapp_pkg_postinst || die "webapp_pkg_postinst failed" +} + +src_test() { + mysql -uroot -p password -e 'create database yeast' + mysql -uroot -p password -e 'grant all privileges on yeast.* to gbrowse@localhost' + mysql -uroot -p password -e 'grant file on *.* to gbrowse@localhost' + mysql -uroot -p password -e 'grant select on yeast.* to nobody@localhost' + + cd /usr/portage/distfiles || die + gzip -d yeast.fasta.gz || die + gzip -d yeast.gff.gz || die + #gzip -d fly.fasta.gz + #gzip -d fly.gff.gz + bp_bulk_load_gff.pl -d yeast -fasta yeast.fasta yeast.gff || die +} |