Importing data from password protected UCSC Genome Browser
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/b9ba5...: 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? 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
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/b9ba5...: 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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Dear Nate, thanks! I got back to my installation and followed your advice, amending my vhost.conf files and I can now, at least, import data from my private UCSC browser into Galaxy. I'll now look into your "next stable release" to get the other direction running. Cheers a lot! Fred On 16/03/2012 16:21, Nate Coraor wrote:
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/b9ba5...: 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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- 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 http://www.networkbio.org
participants (3)
-
Federico De Masi -
Federico De Masi -
Nate Coraor