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Diffstat (limited to 'sci-biology/gbrowse/gbrowse-2.33.ebuild')
-rw-r--r--sci-biology/gbrowse/gbrowse-2.33.ebuild158
1 files changed, 158 insertions, 0 deletions
diff --git a/sci-biology/gbrowse/gbrowse-2.33.ebuild b/sci-biology/gbrowse/gbrowse-2.33.ebuild
new file mode 100644
index 000000000..e2bcfc3be
--- /dev/null
+++ b/sci-biology/gbrowse/gbrowse-2.33.ebuild
@@ -0,0 +1,158 @@
+# 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-${PV}"
+
+DESCRIPTION="The generic genome browser provides a display of genomic annotations on interactive web pages"
+HOMEPAGE="http://gmod.org"
+# mirror://sourceforge/gmod/${MY_P}.tar.gz
+# http://search.cpan.org/CPAN/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz
+SRC_URI="http://search.cpan.org/CPAN/authors/id/L/LD/LDS/${MY_P}.tar.gz
+ test? ( http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz
+ http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )"
+
+LICENSE="Artistic"
+# webapp ebuilds do not set SLOT
+KEYWORDS="~x86 ~amd64"
+IUSE="-minimal svg test" # lwp moby scf
+
+S="${WORKDIR}/${MY_P}"
+
+# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10)
+# TODO: make sure www-servers/apache +cgi
+DEPEND="
+ >=perl-core/Module-Build-0.380.0
+ >=dev-lang/perl-5.8.8
+ dev-perl/Capture-Tiny
+ >=sci-biology/bioperl-1.6
+ >=dev-perl/GD-2.07
+ dev-perl/IO-String
+ virtual/perl-Digest-MD5
+ >=dev-perl/CGI-Session-4.03
+ dev-perl/Statistics-Descriptive
+ >=dev-perl/Bio-Graphics-1.97
+ >=dev-perl/JSON-2.510.0
+ dev-perl/libwww-perl
+ svg? ( dev-perl/GD-SVG )"
+
+# TODO: based on the following message in apache/error_log the list of deps should be longer
+# GBROWSE NOTICE: To enable PDF generation, please enter the directory "/home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache .inkscape .gnome2". To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?ref=chrII;start=90739;end=92028;name=YBL069W;class=Sequence;feature_id=881;db_id=annotations%3Adatabase
+
+# * Bio::DB::BigFile is not installed
+# * Bio::DB::Sam is not installed
+# * DBD::Pg is not installed
+
+
+RDEPEND="${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 "${FILESDIR}"/GBrowseInstall.pm-"${PV}".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 ${FILESDIR}/gbrowse.conf.vhosts.d to /etc/apache2/vhosts.d/"
+
+ sed -i "s#"${D}"##g" "${S}"/install_util/GBrowseInstall.pm || die
+ sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf*
+ sed -i 's#DBI:SQLite:'${D}'/var/www/gbrowse2/databases/#DBI:SQLite:/var/www/gbrowse2/databases/#' "${S}"/install_util/GBrowseInstall.pm || die
+}
+
+pkg_postinst() {
+ webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+
+ einfo "Please run gbrowse_metadb_config.pl to upate SQlite flatfiles or the live database"
+ einfo "This was disabled by "${FILESDIR}"/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm.patch"
+}
+
+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
+}