Difference between revisions of "Blast2GO"
Moskalenko (talk | contribs) |
Moskalenko (talk | contribs) |
||
| Line 55: | Line 55: | ||
====Using HPC GO database from a graphical Blast2GO application==== | ====Using HPC GO database from a graphical Blast2GO application==== | ||
To use the HPC GO database with a graphical Blast2GO interface running locally on your computer: | To use the HPC GO database with a graphical Blast2GO interface running locally on your computer: | ||
| + | #Start an SSH tunnel, forwarding port 3306: | ||
| + | ##In your ssh client, type: ssh -L 3306:10.13.20.209:3306 user@submit.hpc.ufl.edu -N | ||
| + | ##Enter your password at the prompt. | ||
| + | ##The terminal will remain with no input command line, but any MySQL traffic (using port 3306) will be directed to the database server. | ||
#Configure your Blast2GO installation to use the UF HPC datbase: | #Configure your Blast2GO installation to use the UF HPC datbase: | ||
##Select Tools menu and then DB Configuration | ##Select Tools menu and then DB Configuration | ||
| Line 61: | Line 65: | ||
###For DB User: blast2go | ###For DB User: blast2go | ||
###For DB Password: blast2go | ###For DB Password: blast2go | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
|}} | |}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 20:01, 3 December 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
- B2G4PIPE - current Blast2Go directory. This variable can be used for finding the properties file at $B2G4PIPE/conf/blast2go.properties.
Additional Information
Database Releases
- December 2011 - "b2g" database.
- November 2012 - "b2g201211" database.
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.
Using HPC GO database from a graphical Blast2GO application
To use the HPC GO database with a graphical Blast2GO interface running locally on your computer:
- Start an SSH tunnel, forwarding port 3306:
- In your ssh client, type: ssh -L 3306:10.13.20.209:3306 user@submit.hpc.ufl.edu -N
- Enter your password at the prompt.
- The terminal will remain with no input command line, but any MySQL traffic (using port 3306) will be directed to the database server.
- Configure your Blast2GO installation to use the UF HPC datbase:
- Select Tools menu and then DB Configuration
- For DB Host: 127.0.0.1
- For DB Name: b2g201211
- For DB User: blast2go
- For DB Password: blast2go
- Select Tools menu and then DB Configuration