Hi. I was wondering if you have any plans to add the HTGS database option for the blast searches? It could be very helpful for those of us with almost sequenced, but not completed, genomes.

Thanks! M

Mersee Madison-Villar PhD Student, UT Arlington Lab/Office B01 Genomics, Speciation, and Evolutionary Biology

"If evolution is outlawed, only outlaws will evolve"- Jello Biafra ________________________________________ From: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of Nate Coraor [nate@bx.psu.edu] Sent: Monday, November 30, 2009 9:07 AM To: Gunnar Raetsch Cc: Andre Noll; Johannes Woerner; galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] galaxy behind proxy

Gunnar Raetsch wrote:

Hi everybody,

I have a problem with some proxy settings for our galaxy instance. Our admins want to have the server protected better and put it behind a firewall/proxy. That all seems to work after switching on the firewall, but not the external data sources (like biomart or UCSC browser).

I did not find an configuration option for galaxy, so I just use the environment variable http_proxy.

If I try biomart without setting http_proxy, then I get this error message:

The remote data source application may be off line, please try again

later. Error: [Errno socket error] (111, 'Connection refused')

if I set http_proxy to dmzproxy.tuebingen.mpg.de:8080, then I get this error:

Hi Gunnar,

I've never tried this before, but the docs seem to indicate that http_proxy should be specified as a full URL, e.g.: http://dmzproxy.tuebingen.mpg.de:8080

More here:

http://docs.python.org/library/urllib.html

--nate

The remote data source application may be off line, please try again

later. Error: [Errno url error] invalid proxy for http: 'dmzproxy.tuebingen.mpg.de:8080'

These errors appear after finishing with biomart and it tries to send the data back to the galaxy instance.

What is the right way to get these tools to work behind a firewall/proxy?

Thanks a lot for your help in advance,

Gunnar

+-------------------------------------------------------------------+ Gunnar Rätsch http://www.fml.mpg.de/raetsch Friedrich Miescher Laboratory Gunnar.Raetsch@tuebingen.mpg.de Max Planck Society Tel: (+49) 7071 601 820 Spemannstraße 39, 72076 Tübingen, Germany Fax: (+49) 7071 601 801

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Hi Nate & James,

FYI, the problem has been fixed. After adding "http://" in the proxy url and using the right hostname it just worked fine. It did not need any ports to be opened anywhere.

Thanks for your help!

Cheers, Gunnar

On 30.11.2009, at 16:07, Nate Coraor wrote:

Gunnar Raetsch wrote:

...

Hi everybody, I have a problem with some proxy settings for our galaxy instance. Our admins want to have the server protected better and put it behind a firewall/proxy. That all seems to work after switching on the firewall, but not the external data sources (like biomart or UCSC browser). I did not find an configuration option for galaxy, so I just use the environment variable http_proxy. If I try biomart without setting http_proxy, then I get this error message: The remote data source application may be off line, please try again later. Error: [Errno socket error] (111, 'Connection refused') if I set http_proxy to dmzproxy.tuebingen.mpg.de:8080, then I get this error:

Hi Gunnar,

I've never tried this before, but the docs seem to indicate that http_proxy should be specified as a full URL, e.g.: http://dmzproxy.tuebingen.mpg.de:8080

More here:

http://docs.python.org/library/urllib.html

--nate

...

The remote data source application may be off line, please try again later. Error: [Errno url error] invalid proxy for http: 'dmzproxy.tuebingen.mpg.de:8080' These errors appear after finishing with biomart and it tries to send the data back to the galaxy instance. What is the right way to get these tools to work behind a firewall/ proxy? Thanks a lot for your help in advance, Gunnar +-------------------------------------------------------------------+ Gunnar Rätsch http://www.fml.mpg.de/raetsch Friedrich Miescher Laboratory Gunnar.Raetsch@tuebingen.mpg.de Max Planck Society Tel: (+49) 7071 601 820 Spemannstraße 39, 72076 Tübingen, Germany Fax: (+49) 7071 601 801 _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

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