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This is a fork of the orginal BLAST Graphics Viewer used in LiceBase (licebase.org). We have attempted to update the code and fix issues where it was slightly broken or out of date. We have also changed and added some features: - supports only NCBI Blast+ (not WU-blast any more) binaries and options (icluding "Task" parameter) - added support for SAML authentication and logins via Net::SAML module - this change required to add full session management using CGI::Session - changed the configuration file parser to Config::IniFiles to allow for more refined blast database configuration, that also means the config files need to be changed, look at example.conf - primary links can now be set in the configuration DB stanza - GBrowse URLs can now be configured via the configuraton file for each database, they appear below the Blast HSP entry on the result page - all URL parameters are now filtered through String::ShellQuote - script remembers settings for sequence, program, Task, and blast db - these parameters can also be controlled by URL: nph-blast.pl?program=blastn&task=blastn-short - added our own HTML writer module because we need to be able to configure the output to enable these features - added a mechanism that can connect to a CHADO backend to retrieve sequence files - added a mechanism that can write a feature location entry derived from BLAST coordinates to CHADO for sequences retrieve from CHADO - script reads the location of the CSS file from the configuration - script can be called with embedd=1 parameter, then the script will not display greetings, title, and login and logout information - put the image generation in an eval - 'fixed' anchor links between graphics and textual result, works now but only for Nucleotide sequences TODOs: - fix hyperlinks between graphics and textual result for non DNA - remove all remnants of outdated WU-blast, in favor of open-source NCBI blast - the original 'synchroneous job handling' is naively implemented. * result page can time out * no wait indicator * no job management, easy to overload server -> implement result page in Ajax with 'spinner' -> integrate one/many proper queueing system, e.g. OGE via DRMAA - allow for more than a single query sequence ================================= Original README ============================================= The BLAST Graphic Viewer provides a graphical visualization of the regions contained within HSPs relative to the query sequence. This distribution includes sample databases and a BLAST Search form. It is a component of the Generic Model Organism Systems Database project (GMOD.sourceforge.net). - For a demo, go to http://seq.yeastgenome.org/cgi-bin/GMOD/nph-blast.pl - To download the Washington University BLAST(WU-BLAST), go to http://blast.wustl.edu/ - To download the BLAT programs, go to http://www.genomeblat.com/genomeblat/ - To download the NCBI BLAST programs, go to http://www.ncbi.nlm.nih.gov/BLAST/ - To download the sample databases, go to ftp://genome-ftp.stanford.edu/pub/people/programmer/gmod/ - This graphic module will support BLASTN, BLASTP, BLASTX, TBLASTX, TBLASTN, BLAT, and TBLATN. For the databases, it will support any fasta- formated datasets (i.e., nr, nt, etc). - The cgi program (nph-blast.pl) included in this distribution is used to display a BLAST/BLAT search form and search result for WU-BLAST or BLAT. It can be copied into any directory under your cgi-bin. You can update the $CONF_FILE variable in the top of this script to point to your own location of the configuration file. - To set your own locations for blast programs, databases, filters, and matrix, and tmp directory for storing the png file, please see the configuration file (conf/Blast.conf). You can copy this file (Blast.conf) into any world readable directories. - To install this module on your own system, issue the following commands: perl Makefile.PL make make install - Prerequisites: this module runs on top of several software packages. These packages must be installed before you can run this viewer. A) Apache Web Server -- http://www.apache.org The Apache web server is the industry standard open source web server for Unix and Windows systems. B) Perl 5.005 or higher-- http://www.cpan.org The Perl language is widely used for web applications. C) Standard Perl modules -- http://www.cpan.org The following Perl modules must be installed for the Blast Graphic Viewer to work. They can be found on CPAN: File::Listing File::Basename GD CGI D) Bioperl modules -- http://www.bioperl.org The following Bioperl modules must be installed for this viewer to work. Bio::Root::IO Bio::SearchIO Bio::SearchIO::Writer::HTMLResultWriter This is a free software. You can use it under the same terms as Perl itself. Please see DISCLAIMER for limitations ... Support is available from the discussion groups and mailing lists at www.gmod.org Shuai Weng & SGD team email@example.com www.yeastgenome.org Nov. 15, 2005