On Feb 7, 2012, at 5:52 AM, Federico De Masi wrote:

> Dear colleagues,
> 
> I have been struggling with this issue for quite a while now, and I don't 
> seem to find a solution (neither in situ nor in webo).
> 
> here it is:
> 
> Because of the confidentiality of our data, I have setup both a Galaxy server 
> and a UCSC Genome Browser locally on my server. Both are run through Apache, 
> using the same .htpasswd authentication method and file (ie: same 
> usernmae/password combo for each).
> 
> Everything works great except that I do not seem to be able to send/receive 
> data from Galaxy to UCSC and vice versa.
> 
> When I try to "get data" from UCSC main (my local instance), I get the 
> followin error:
> 
> "Tool execution generated the following error message:
> The remote data source application may be off line, please try again later. 
> Error: EOF when reading a line
> The tool produced the following additional output:
> Enter username for SG at 127.0.0.1:"
> 
> where SG is the AuthName in vhost.conf and 127.0.0.1 is UCSC's IP.
> 
> Whenever I try to to send data to UCSC ("Display at UCSC main" in the history 
> boxes), I get this guy:
> "Expected 200
> http://127.0.0.3/display_application/48916fac0de9a85d/ucsc_bigwig/main/b9ba5eb40e0fec32/param/track:
>  
> 401 Authorization Required"
> 
> Where 127.0.0.3 is galaxy's IP.
> 
> I have:
> - hardcoded username:passowrd on UCSC's "send to galaxy" routine but to no 
> avail
> - hardcode username:passowrd on Galaxy's definiton of UCSC's "main" URL, but 
> to no avail
> - I have removed UCSC authentication, and everything works fine
> - I have kept UCSC authentication and let Galaxy "open", doesn't work
> - I remove authentication to both servers, and it all works cool.
> 
> Somehow, Galaxy doesn't like to talk to a protected UCSC browser.
> 
> I'll be happy to post my vhost.conf files if needed.
> 
> Can anyone help, please?

Hi Fred,

Sorry for not replying sooner.  I have just committed a fix that should make 
this a bit easier.  Previously, you had to modify a bit of the Galaxy source to 
allow your UCSC server to access data in Galaxy.  I've made this in to an 
option in the config file, and the details are in the wiki documentation at:

    http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy

This change will be available in our next stable release.

For the reverse direction (fetching data from UCSC), if you're proxying your 
UCSC server via Apache, I'd suggest using the "Satisfy Any" method shown in our 
documentation to allow the Galaxy server to bypass authentication to access the 
UCSC server.  Assuming your UCSC server has its own VirtualHost, you'd do 
something like:

    AuthType your_authtype
    ... other site-specific authentication directives ...
    Satisfy Any
    Order deny,allow
    Deny from all
    Allow from galaxy.example.org

Note that you need both - The Galaxy server needs an "Allow" to talk to the 
UCSC server (in the UCSC vhost) and the UCSC server needs an "Allow" to talk to 
the Galaxy server (in the Galaxy vhost).

--nate

> 
> Thanks a lot,
> 
> Fred
> 
> -- 
> Federico De Masi, PhD,
> Assistant Professor
> The Technical University of Denmark - DTU
> Center for Biological Sequence Analysis - CBS
> Kemitorvet 208/002
> DK-2800 KGS. LYNGBY, DENMARK
> Telephone: (+45) 45 25 24 21
> Fax: (+45) 45 93 15 85
> http://rg.cbs.dtu.dk
> ___________________________________________________________
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