Galaxy Behind Proxy

Question: Galaxy Behind Proxy

9.0 years ago by

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: 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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modified 9.0 years ago by Nate Coraor ♦ 3.2k • written 9.0 years ago by Gunnar Raetsch • 60

9.0 years ago by

Nate Coraor ♦ 3.2k

United States

Nate Coraor ♦ 3.2k wrote:

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

ADD COMMENT • link written 9.0 years ago by Nate Coraor ♦ 3.2k

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 ________________________________________ To: Gunnar Raetsch Cc: Andre Noll; Johannes Woerner; galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] galaxy behind proxy 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 _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

ADD REPLY • link written 9.0 years ago by Madison-Villar, Mercedita J • 20

Mersee: Could you be a bit more specific (can you give me a link) about the HTGS database? We can add it then. Thanks! anton galaxy team Anton Nekrutenko http://nekrut.bx.psu.edu http://galaxyproject.org

ADD REPLY • link written 9.0 years ago by Anton Nekrutenko ♦ 1.7k

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

ADD REPLY • link written 9.0 years ago by Gunnar Raetsch • 60

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