error listing MsigDB files

[Harmanpreet singh]

Hi 

We are getting issues using GSEA, which was recently installed. We contacted the IT department, and they said for the last 30 days show that 100% of the traffic has been allowed.

See below:

Error listing MSigDB files:
Read timed out

This might be due to your network's firewall rules.
MSigDB files can be manually downloaded from www.gsea-msigdb.org/gsea/downloads.jsp

Use 'Load Data' to provide access to local files.
Choose gene sets from other tabs.

Please suggest how we should use it.

Thanks

  

[David Eby]

Hello Harmanpreet,

The GSEA Desktop accesses these files using FTP (at ftp.broadinstitute.org) rather than HTTP (at www.gsea-msigdb.org).  Many IT departments block FTP traffic and generally treat "traffic" as being only HTTP.  A check on that FTP site today shows that it is still accessible from the general internet, so this is the likely issue.

The workaround is as described in that message: you can find our GMT and CHIP files from the listed Downloads page, and then use the Load Data screen to import them into GSEA for execution as usual.

We have it on our agenda for a future release to remove the FTP dependency, but for now this is the only automatic download option available.

Regards,

David

David Eby
www.gsea-msigdb.org

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[Harmanpreet singh]

Hi David 

Thanks for the reply.

Do we use a specific port or address that we need to add to our firewall or network for access? Is this works.

Thanks

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[David Eby]

Hello Harmanpreet,

You would need your IT department to open FTP access (on the default FTP ports) for ftp.broadinstitute.org.  If they are unwilling to do that, I would recommend the workaround described earlier.

GMT & CHIP files imported through Load Data will show up under the tabs "Local GMT/GMX" and "Local Chips", respectively.

- David

David Eby
www.gsea-msigdb.org

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[Harmanpreet singh]

Thanks, David!

This helped.

Best

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[Franklin Pierre]

It was really helpful