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Diffstat (limited to 'sci-biology/gbrowse/gbrowse-2.48.ebuild')
| -rw-r--r-- | sci-biology/gbrowse/gbrowse-2.48.ebuild | 200 |
1 files changed, 200 insertions, 0 deletions
diff --git a/sci-biology/gbrowse/gbrowse-2.48.ebuild b/sci-biology/gbrowse/gbrowse-2.48.ebuild new file mode 100644 index 000000000..754cc9e5e --- /dev/null +++ b/sci-biology/gbrowse/gbrowse-2.48.ebuild @@ -0,0 +1,200 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ +EAPI="2" + +inherit perl-module webapp + +MY_P="GBrowse-${PV}" + +DESCRIPTION="Display of genomic annotations on interactive web pages" +HOMEPAGE="http://gmod.org/" +# mirror://sourceforge/gmod/${MY_P}.tar.gz +# mirror://cpan/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz +SRC_URI=" + mirror://cpan/authors/id/L/LD/LDS/${MY_P}.tar.gz + test? ( + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2 + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz + http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )" + +LICENSE="Artistic" +# webapp ebuilds do not set SLOT +KEYWORDS="~x86 ~amd64" +IUSE="cgi fastcgi minimal mysql pdf postgres svg test" # lwp moby scf + +S="${WORKDIR}/${MY_P}" + +# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10) +# how about mod_fcgi and dev-libs/fcgi and mod_scgi? +DEPEND="!!sci-biology/GBrowse + >=perl-core/Module-Build-0.380.0 + >=dev-lang/perl-5.8.8 + dev-perl/Capture-Tiny + >=sci-biology/bioperl-1.6.901 + >=dev-perl/GD-2.07 + dev-perl/IO-String + virtual/perl-Digest-MD5 + >=dev-perl/CGI-Session-4.03 + dev-perl/Statistics-Descriptive + >=dev-perl/Bio-Graphics-2.26 + >=dev-perl/JSON-2.510.0 + dev-perl/TermReadKey + dev-perl/libwww-perl + svg? ( dev-perl/GD-SVG ) + pdf? ( media-gfx/inkscape ) + mysql? ( dev-perl/DBD-mysql ) + postgres? ( dev-perl/DBD-Pg ) + sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src + +# TODO: based on the following message in apache/error_log the list of deps should be longer +# GBROWSE NOTICE: To enable PDF generation, please enter the directory "/home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache .inkscape .gnome2". To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?ref=chrII;start=90739;end=92028;name=YBL069W;class=Sequence;feature_id=881;db_id=annotations%3Adatabase + +RDEPEND="${DEPEND} + >=www-servers/apache-2.0.47 + fastcgi? ( dev-libs/fcgi ) + 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 + postgres? ( >=dev-perl/Bio-DB-Das-Chado-0.32 ) + >=dev-perl/Bio-SamTools-1.29 + >=dev-perl/Bio-BigFile-1.06 + <=sci-biology/primer3-2 + )" + +src_prepare() { + sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die "Failed to kill the interactive behavior of install_util/GBrowseInstall.pm" + sed -i 's/process_/bp_process_/g' INSTALL || die "Failed to prepend bp_ prefix to INSTALL file" + epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to apply GBrowseInstall.pm-"${PV}".patch" + epatch "${FILESDIR}"/destdir.patch || die "Failed to apply destdir.patch" + epatch "${FILESDIR}"/fix-PNG-export.patch || die "Failed to apply fix-PNG-export.patch" + epatch "${FILESDIR}"/symlink.patch || die "Failed to apply symlink.patch" + epatch "${FILESDIR}"/gbrowse_metadb_config.pl.patch || die "Failed to apply gbrowse_metadb_config.pl.patch" + epatch "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch || die "Failed to apply disable-gbrowse_metadb_config.pl.patch" + for f in conf/synteny/wild_rice_synteny.conf conf/synteny/rice_synteny.conf conf/GBrowse.conf \ + htdocs/tutorial/tutorial.html htdocs/index.html lib/Bio/Graphics/Browser2/Action.pm \ + Changes; do + sed -i 's#/var/lib/gbrowse2#/var/db/gbrowse2#' $f || die "Failed to rewrite /var/lib/gbrowse2 to /var/db/gbrowse2 in $f" + done + for f in htdocs/index.html; do + sed -i 's#/usr/lib/cgi-bin/gb2#/usr/share/webapps/gbrowse/"${PV}"/htdocs/cgi-bin#' $f || die "Failed to rewrite /usr/lib/cgi-bin/gb2 to /usr/share/webapps/gbrowse/"${PV}"/htdocs/cgi-bin in $f" + done +} + +src_configure() { + # GBROWSE_ROOT is the root path in SRC_URI to be prepended + # /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf + webapp_src_preinst + perl Makefile.PL \ + HTDOCS="${MY_HTDOCSDIR}" \ + CGIBIN="${MY_HTDOCSDIR}"/cgi-bin \ + CONF="${MY_HTDOCSDIR}"/etc/gbrowse \ + PACKAGE_DIR="${D}" \ + INSTALLDIRS=vendor \ + GBROWSE_ROOT="gbrowse" \ + DESTDIR="${D}" \ + DATABASES="/var/db/gbrowse2/databases" \ + PERSISTENT="/var/db/gbrowse2" \ + 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 "${S}"/INSTALL + webapp_src_install || die "Failed running webapp_src_install" + + # should create a /etc/init.d/ startup script based on this + # /var/tmp/portage/sci-biology/gbrowse-2.03/work/GBrowse-2.03/etc/init.d/gbrowse-slave + + mkdir -p "${D}"/var/tmp/gbrowse2/images + chown -R apache.apache "${D}"/var/tmp/gbrowse2 + + # mkdir -p "${D}"/var/www/localhost/htdocs/gbrowse || die + # ln -s "${D}"/var/tmp/gbrowse2/images "${D}"/usr/share/webapps/gbrowse/"${PV}"/htdocs/i || die + + # whole "${D}"/var/db/gbrowse2 has to be owned by apache.apache otherwise: + # 1. you hit an error that /var/db/gbrowse2/sessions/cgisess.db.lck + # [no, it is not enough chown -R apache.apache /var/db/gbrowse2/sessions, the parent dir has to be apapche.apache as well] + # 2. even if you set /var/db/gbrowse2 to apache.apache still it is not enough, you will get + # [Tue Jan 17 14:59:40 2012] [error] [client 127.0.0.1] Use of uninitialized value $label in lc at /usr/lib/perl5/vendor_perl/5.12.4/i686-linux-thread-multi/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm line 34., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse/yeast/ + + mkdir -p "${D}"/var/db/gbrowse2 + mkdir -p "${D}"/var/db/gbrowse2/databases + mkdir -p "${D}"/var/db/gbrowse2/sessions "${D}"/var/db/gbrowse2/userdata + chown -R apache.apache "${D}"/var/db/gbrowse2 # it has to be owned by apache.apache otherwise /var/db/gbrowse2/sessions/cgisess.db.lck cannot be created although /var/db/gbrowse2/sessions is owner by apache.apache + + einfo "Dropping trailing 'databases' from db_variable in conf/GBrowse.conf" + sed -i 's#/var/db/gbrowse2/databases#/var/db/gbrowse2#' conf/GBrowse.conf || die "Failed to dropping trailing 'databases' from db_variable in conf/GBrowse.conf" + + 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 do" + einfo "cp -i ${FILESDIR}/gbrowse.conf.vhosts.d /etc/apache2/vhosts.d/gbrowse.conf" + + sed -i "s#"${D}"##g" "${S}"/install_util/GBrowseInstall.pm || die + sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf* + sed -i 's#DBI:SQLite:'${D}'/var/lib/gbrowse2/databases/#DBI:SQLite:/var/db/gbrowse2/databases/#' "${S}"/install_util/GBrowseInstall.pm || die +} + +pkg_postinst() { + webapp_pkg_postinst || die "webapp_pkg_postinst failed" + + einfo "Please run gbrowse_metadb_config.pl to update SQLite flatfiles of the live database." + einfo "d='/usr/share/webapps/gbrowse/${PV}/htdocs/etc/gbrowse'; for f in \$d/*.conf.new; do \ " + einfo " mv -i \$f \$d/\`basename \$f .new\`; done" + + einfo "Fix also the other copy of the file:" + einfo "d='/var/www/localhost/htdocs/gbrowse/etc/gbrowse'; for f in \$d/*.conf.new; do \ " + einfo " mv -i \$f \$d/\`basename \$f .new\`; done" +} + +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 +} |