assembly hub + blat port(?) configuration issue

[Cook, Malcolm]

I have a an assembly hub being served from linux host named, say, “data.stowers.org”, which resides in our networks DMZ.

 

The hub displays perfectly within genome browser at http://genome.ucsc.edu 

 

It also displays perfectly within a locally hosted instance of GBIB running on host, say, ‘genome.sgc.loc’ which sits within our firewall.

 

I’ve now enabled blat by running gfserver using ports 17000 and 17001 on the 2bit files  data.stowers.org and accordingly added the blat and transBlat entries to the genome.txt file.

 

Blat now works perfectly within my locally hosted GBIB,

 

Alas, it does NOT when the hub is displayed at UCSC, where I get:

 

Warning/Error(s):

TCP non-blocking connect() to tracks.stowers.org timed-out in select() after 10000 milliseconds - Cancelling!

Operation now in progress

Sorry, the BLAT/iPCR server seems to be down. Please try again later.

 

I assume there is a port issue and I need to tell my network guys (cc:ed) to open ports 17000 and 17001 to genome.ucsc.org.

 

Is this correct?

 

Assuming it is, my network guys tell me “Our firewall cannot do DNS for access control list. We will have to know what ip addresses to allow.  “

 

Trying to look it up, I see:

 

$ nslookup genome.ucsc.edu

 

Non-authoritative answer:

genome.ucsc.edu            canonical name = genome.cse.ucsc.edu.

Name:  genome.cse.ucsc.edu

Address: 128.114.119.135

Name:  genome.cse.ucsc.edu

Address: 128.114.119.136

Name:  genome.cse.ucsc.edu

Address: 128.114.119.131

Name:  genome.cse.ucsc.edu

Address: 128.114.119.132

Name:  genome.cse.ucsc.edu

Address: 128.114.119.133

Name:  genome.cse.ucsc.edu

Address: 128.114.119.134        

 

 

What should I tell my network guys?   128.114.119.13*?

 

Thanks

 

Malcolm Cook

Computational Biology

Stowers Institute for Medical Research

1000 E 50^th Street

Kanas City, MO 64110

(816) 926-4449

m...@stowers.org

 

[Brian Lee]

Dear Malcolm Cook,

Thank you for using the UCSC Genome Browser, Track Hubs, and trying the new BLAT feature on Assembly Hubs, and your excellently researched question!

You are absolutely correct.  We suggest users ask if their admins can add this IP range as exceptions that are not limited: 128.114.119.*

That will cover our U.S. genome.ucsc.edu site, which is an alias for genome.cse.ucsc.edu.

Also, in case you may wish to use our European Mirror genome-euro.ucsc.edu, which is is an alias for genome-browser-mirror.dhcp.uni-bielefeld.de, you would want to include this IP also to the exception list: 129.70.40.120

Thank you again for writing in with this wonderfully worded question!  The documentation regarding adding BLAT to Assembly Hubs will be updated with these IP ranges to help future users.

Thank you again for your inquiry and using the UCSC Genome Browser and helping us improve our documentation. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genome Bioinformatics Group

--

[Cook, Malcolm]

Brian – Perfect – All is good.

!Malcolm