Difference between revisions of "Blast2GO"
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[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]] | [[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]] | ||
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<!--Main settings - REQUIRED--> | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|blast2go}} | |{{#vardefine:app|blast2go}} | ||
|{{#vardefine:url|http://www.blast2go.com/b2ghome}} | |{{#vardefine:url|http://www.blast2go.com/b2ghome}} | ||
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | ||
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
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===Serial=== | ===Serial=== | ||
*{{#var:app}} | *{{#var:app}} | ||
| − | {{#if: {{#var: exe}}|== | + | ==System Variables== |
| + | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
| + | <!--Additional--> | ||
| + | {{#if: {{#var: exe}}|==Additional Information== | ||
How to run with default properties: use the b2g4pipe wrapper, which is equivalent to | How to run with default properties: use the b2g4pipe wrapper, which is equivalent to | ||
"java -Xms64m -Xmx500m -cp $B2G4PIPE/*:$B2G4PIPE/ext/*: es.blast2go.prog.B2GAnnotPipe | "java -Xms64m -Xmx500m -cp $B2G4PIPE/*:$B2G4PIPE/ext/*: es.blast2go.prog.B2GAnnotPipe | ||
Revision as of 17:45, 10 August 2012
Description
The Blast2GO Pipeline Version (B2G4Pipe) runs Blast2GO without graphical interface. The pipeline accepts BLAST and InterProScan results and parses the XML belonging to each sequence (provided in FASTA format). The program extracts GO terms to each obtained blast hit by mapping to existent annotation associations. An annotation rule finally assigns GO terms to the query sequence. Additionally you can add domain/motif based GO term obtained through InterProScan searches. Deduced GO terms are added to the BLAST based annotations, always taking into account the GO True-Path-Rule.
The output files generated by B2G4Pipe are equivalent to the file generated by the desktop application.
Required Modules
Serial
- blast2go
System Variables
- HPC_{{#uppercase:blast2go}}_DIR - installation directory
Additional Information
How to run with default properties: use the b2g4pipe wrapper, which is equivalent to "java -Xms64m -Xmx500m -cp $B2G4PIPE/*:$B2G4PIPE/ext/*: es.blast2go.prog.B2GAnnotPipe -prop $B2G4PIPE/b2gPipe.properties -v -annot -dat -img -ips ipsr -annex -goslim -wiki $B2G4PIPE/html_template.html" and only requires the input and output file names such as : -in input.xml -out results
Additional wrappers are provided for various memory settings (See Memory Table for a table of memory vs. number of sequences that can be annotated) such as b2g4pipe-1000, b2g4pipe-1500, b2g4pipe-2000, and b2g4pipe-4000.
If you need to change the command line switches beyond the existing wrappers then you'll have to build your own appropriate command line.
To use the HPC GO database with a graphical Blast2go interface configure your Blast2go installation and use the '10.13.16.10' database host with 'blast2go' user and 'blast2go' password. You will have to create an ssh tunnel to the database host as it's not accessible otside of the HPC cluster.