Run Blast2Go offline

[Slientinverse85]

I have successfully installed and run a localized Blast2Go using Java Web Start. However my professor want to run Blast2Go offline on a sever with no internet connection. Can this be done?

[angeloulivieri]

I think that it's not possible. The java web start application is only a client software. So it have to be connected to the Blast2GO server. If you wanna do the analysis on your server only, without internet connection, you have to download blast software to your own machine.
I'm new about blast so.. could anyone correct me if i'm wrong? :-P

[maubp]

I have successfully installed and run a localized Blast2Go using Java Web Start. However my professor want to run Blast2Go offline on a sever with no internet connection. Can this be done?

Yes. You can download the JAVA application itself - that's the easy part. Next you must do the BLAST searches off-line - you can download the NCBI standalone BLAST tools and the NR database to do this. The hard part is you must also setup a local BLAST2GO database to map the BLAST results to GO terms. See http://www.blast2go.com/b2glaunch/re.../35-localb2gdb and other pages on their website.

[Slientinverse85]

Yes. You can download the JAVA application itself - that's the easy part. Next you must do the BLAST searches off-line - you can download the NCBI standalone BLAST tools and the NR database to do this. The hard part is you must also setup a local BLAST2GO database to map the BLAST results to GO terms. See http://www.blast2go.com/b2glaunch/re.../35-localb2gdb and other pages on their website.

I already have setup a local Blast2Go database. But do not understand the other steps. Can you explain them more clearly? or give me the webpages so I can found what I need online?

[maubp]

I already have setup a local Blast2Go database. But do not understand the other steps. Can you explain them more clearly? or give me the webpages so I can found what I need online?

Where are you getting stuck?

A key point is you must change the Blast2GO configuration (e.g. via the GUI, or editing the configuration file manually) to connect to your local database (with the appropriate password etc) rather than the server in Spain. If your local database is on a separate machine, you may also need to check your firewall settings.

[Slientinverse85]

Where are you getting stuck?

A key point is you must change the Blast2GO configuration (e.g. via the GUI, or editing the configuration file manually) to connect to your local database (with the appropriate password etc) rather than the server in Spain. If your local database is on a separate machine, you may also need to check your firewall settings.

I already evething in http://www.blast2go.com/b2glaunch/re.../35-localb2gdb. But I still need to run Java Web Start in order to use Blast2Go. I need to be able to use it without JWS.

Do you Know if the step need to configure Blast2Go so it connects to the local database is writen in http://www.blast2go.com/b2glaunch/re.../35-localb2gdb?

Which JAVA application do I need to download? Is the NCBI standalone BLAST tool wwwBlast? Finally where can I find the NR database?

[maubp]

I already evething in http://www.blast2go.com/b2glaunch/re.../35-localb2gdb. But I still need to run Java Web Start in order to use Blast2Go. I need to be able to use it without JWS.

Have you tried downloading the main Blast2GO JAR file, and running that via Java at the command line?

Do you Know if the step need to configure Blast2Go so it connects to the local database is writen in http://www.blast2go.com/b2glaunch/re.../35-localb2gdb?

Yes, step 7 talks about this.

Which JAVA application do I need to download?

Blast2GO?

Is the NCBI standalone BLAST tool wwwBlast?

I don't know if you could use wwwBLAST which is a local webserver, or not.

I use the command line version of NCBI BLAST, I would suggest using BLAST+ since the NCBI have now discontinued the older 'legacy' BLAST suite:
ftp://ftp.ncbi.nlm.nih.gov/blast/exe...blast+/LATEST/

Finally where can I find the NR database?

ftp://ftp.ncbi.nlm.nih.gov/blast/db/

[Slientinverse85]

What do I need to download in the NR database?

[maubp]

What do I need to download in the NR database?

Would you like a spoon?

There is a README file there which explains this. You will need nr.00.tar.gz, ..., nt.12.tar.gz (at the moment - as the NR database grows it will in future come in more pieces). Each of these is a tarball (compressed file) which you must unpack in the same directory.

You should read the BLAST+ documentation as soon as possible.

[Slientinverse85]

where do I find the main Blast2GO JAR file? I didn't find it on the Blast2Go website.

[maubp]

where do I find the main Blast2GO JAR file? I didn't find it on the Blast2Go website.

The website does document the webstart URL, and how to adjust the memory - e.g. 1GB or 1024MB with:

javaws http://www.blast2go.com/webstart/makeJnlp.php?mem=1024

If you look at the Java webstart XML it is clear where the blast2go.jar itself is downloaded from:

$ curl http://www.blast2go.com/webstart/makeJnlp.php?mem=1024
<jnlp spec="1.0+" codebase="http://www.biobam.com/webstart" href="http://www.biobam.com/webstart/makeJnlp.php?mem=1024">
<information>
<title>Blast2GO 1024M</title>
<vendor>BioBam Bioinformatics S.L.</vendor>
<homepage href="http://www.blast2go.com"/>
<description>Blast2GO 1024M</description>
<description kind="short">Blast2GO 1024M</description>
<icon href="splash.gif"/>
<offline-allowed/>
</information>
<security>
<all-permissions/>
</security>
<resources>
<j2se version="1.6+" initial-heap-size="64m" max-heap-size="1024M"/>
<jar href="ext/blast2go.jar"/>
<jar href="ext/biojava-1.3.1.jar"/>
...

i.e. The main file is here: http://www.biobam.com/webstart/ext/blast2go.jar - but with my limited Java knowledge this doesn't seem designed to be run directly.

This is different to Blast2GO for Pipelines (b2g4pipe) which comes as a JAR file intended to be run directly (which is what we are using locally via a Galaxy wrapper to serve as an end user interface, talking to either a local Blast2GO database or the one in Spain):

http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip

[Slientinverse85]

What do you mean when you said to "do the BLAST searches off-line."?

[maubp]

What do you mean when you said to "do the BLAST searches off-line."?

I mean don't use the NCBI BLAST servers over the internet, instead use a local copy of the BLAST+ programs and a local copy of the database - in this case the NR database download from the NCBI FTP site.

[Slientinverse85]

Blast2Go for pipelines doesn't work on my mac, Should I use another?

I have installed Blast+ onto my computer, but I can't find the installed files, what should I do?

[maubp]

Regarding installing and using BLAST+, I suggest you first search these forums (and try Google), and if you are still stuck start a new thread about that. Remember to include important details like which OS you are using, where you downloaded BLAST+ from (the URL including the filename), and how you installed it.