Difference between revisions of "Blast2GO"

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m (Text replace - "Usage policy" to "Usage Policy")
 
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__NOTOC____NOEDITSECTION__
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[[Category:Software]][[Category:Biology]][[Category:Genomics]]
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[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
 
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<!-- ########  Template Configuration ######## -->
 
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<!--Edit definitions of the variables used in template calls
 
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Required variables:
 
−
app - lowercase name of the application e.g. "amber"
 
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url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
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Optional variables:
 
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INTEL - Version of the Intel Compiler e.g. "11.1"
 
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MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
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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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<!--Compiler and MPI settings - OPTIONAL -->
 
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|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
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|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
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<!--Choose sections to enable - OPTIONAL-->
 
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|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
 
|{{#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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{{#if: {{#var: url}}|
 
{{#if: {{#var: url}}|
 
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
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__NOTOC____NOEDITSECTION__
 
The Blast2GO Pipeline Version (B2G4Pipe) runs Blast2GO without graphical
 
The Blast2GO Pipeline Version (B2G4Pipe) runs Blast2GO without graphical
 
interface. The pipeline accepts BLAST and InterProScan results and parses
 
interface. The pipeline accepts BLAST and InterProScan results and parses
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The output files generated by B2G4Pipe are equivalent to the file generated
 
The output files generated by B2G4Pipe are equivalent to the file generated
 
by the desktop application.
 
by the desktop application.
 +
 
<!--Modules-->
 
<!--Modules-->
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{{#if: {{#var: mod}}|==Execution Environment and Modules==
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==Environment Modules==
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{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
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{{#if: {{#var: exe}}|==How To Run==
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==System Variables==
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How to run with default properties: use the b2g4pipe wrapper, which is equivalent to   
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* 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''.
 +
<!--Additional-->
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{{#if: {{#var: exe}}|==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 or through OOD. 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. '<code>-wiki PE/html_te$B2G4PImplate.html</code>'
 +
;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
 
"java -Xms64m -Xmx500m -cp $B2G4PIPE/*:$B2G4PIPE/ext/*: es.blast2go.prog.B2GAnnotPipe
 
-prop $B2G4PIPE/b2gPipe.properties -v -annot -dat -img -ips ipsr -annex
 
-prop $B2G4PIPE/b2gPipe.properties -v -annot -dat -img -ips ipsr -annex
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-goslim -wiki $B2G4PIPE/html_template.html" and only requires the input and  
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-goslim -wiki PE/html_te$B2G4PImplate.html" and only requires the input and  
 
output file names such as : -in input.xml -out results
 
output file names such as : -in input.xml -out results
  
−
Additional wrappers are provided for various memory settings (See [http://www.blast2go.com/b2glaunch/start-blast2go 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.
+
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.
 
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
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====Using HPC GO database from a graphical Blast2GO application====
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your Blast2go installation and use the '10.13.16.10' database host with
+
To use the HPC GO database with a graphical Blast2GO interface running locally on your computer:
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'blast2go' user and 'blast2go' password. You will have to create an ssh
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* Start an SSH tunnel, forwarding port 3306:
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tunnel to the database host as it's not accessible otside of the HPC
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#In your ssh client, type: ssh -L 3306:blast2godb.ufhpc:3306 user@hpg.rc.ufl.edu -N
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cluster.
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#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
 
|}}
 
|}}
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 14:08, 16 March 2023

Description

blast2go website  

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.

Environment Modules

Run module spider blast2go to find out what environment modules are available for this application.

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 or through OOD. 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'
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:
  1. In your ssh client, type: ssh -L 3306:blast2godb.ufhpc:3306 user@hpg.rc.ufl.edu -N
  2. Enter your password at the prompt.
  3. 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
      1. For DB Host: localhost
      2. For DB Name: b2g201503
      3. For DB User: blast2go
      4. For DB Password: blast2go




Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=Blast2GO&oldid=27653"