Difference between revisions of "Blast2GO"
Moskalenko (talk | contribs) |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
||
| (One intermediate revision by the same user not shown) | |||
| Line 36: | Line 36: | ||
*{{#var:app}} | *{{#var:app}} | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
* B2G4PIPE - current Blast2Go directory. This variable can be used for finding the properties file at ''$B2G4PIPE/conf/blast2go.properties''. | * B2G4PIPE - current Blast2Go directory. This variable can be used for finding the properties file at ''$B2G4PIPE/conf/blast2go.properties''. | ||
<!--Additional--> | <!--Additional--> | ||
| Line 77: | Line 77: | ||
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: | * Start an SSH tunnel, forwarding port 3306: | ||
| − | #In your ssh client, type: ssh -L 3306:blast2godb.ufhpc:3306 user@ | + | #In your ssh client, type: ssh -L 3306:blast2godb.ufhpc:3306 user@hpg.rc.ufl.edu -N |
#Enter your password at the prompt. | #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. | #The terminal will remain with no input command line, but any MySQL traffic (using port 3306) will be directed to the database server. | ||
Revision as of 21:03, 6 December 2019
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_BLAST2GO_DIR - installation directory
- B2G4PIPE - current Blast2Go directory. This variable can be used for finding the properties file at $B2G4PIPE/conf/blast2go.properties.
Additional Information
Database Releases
- December 2011 - "b2g" database.
- November 2012 - "b2g201211" database.
- November 2013 - "b2g201311" database.
- March 2015 - "b2g201503" database.
Using B2G4PIPE at UFRC
Please note that the Blast2Go team considers b2go4pipe obsolete and unsupported. If you need the results that the current Blast2Go software produces you should consider purchasing a license. You can use the database we host on HiPerGator with the Blast2Go GUI application running on your local computer on UF campus or connected via VPN to UF Campus. As far as we know Blast2Go command-line tools still have node-locked licenses, so it is not feasible to run them on a computer cluster like HiPerGator.
Keeping the above in mind it is still possible to run B2G4PIPE and generate Gene Ontologies for your BLAST data. Below are considerations and modifications you need to make to have a successful run.
- Blast2GO can not reach the Internet
-
- This warning should be ignored. It's likely due to a server check b2go4pipe does at the beginning of a run.
- Changed property MainGui.Workspace from results.annot to test_cit.annot /apps/blast2go/2.5.0-20120705/b2gPipe201503.properties (Permission denied)
-
- It looks like you need a local copy of b2gPipe201503.properties. Copy it to your current working directory and use it when running B2GO4PIPE
- Problem creating wiki file
- html_template.html (No such file or directory):
- See the default run example below. You have to provide the full path to the template file i.e. '
-wiki PE/html_te$B2G4PImplate.html'
- See the default run example below. You have to provide the full path to the template file i.e. '
- Can not parse BLAST XML because can not find information about the used version!
-
- Since b2go4pipe has not been updated in years it likely produces an error when encountering newer BLAST versions in the BLAST xml file. Edit the xml file to change, for example,
<BlastOutput_version>BLASTP 2.5.1+</BlastOutput_version>
to
<BlastOutput_version>BLASTP 2.2.26</BlastOutput_version>
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 $B2G4PIPE/b2gPipe.properties -v -annot -dat -img -ips ipsr -annex -goslim -wiki PE/html_te$B2G4PImplate.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 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:blast2godb.ufhpc:3306 user@hpg.rc.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 UFRC datbase:
- Select Tools menu and then DB Configuration
- For DB Host: localhost
- For DB Name: b2g201503
- For DB User: blast2go
- For DB Password: blast2go
- Select Tools menu and then DB Configuration