Hello Jim

Re your problem #1 (UCSC browser appears to be blocked), I've seen something similar with our local Galaxy instance, which is also served via https.


In our case I believe this is actually a browser issue: the latest version of Firefox silently blocks mixed secure and insecure content:

https://blog.mozilla.org/tanvi/2013/04/10/mixed-content-blocking-enabled-in-firefox-23/

(I think Chrome and IE do something similar, although IE at least gives a warning.)

The workaround is either to disable mixed content blocking (not trivial in Firefox, and probably not a good idea in general), or to do something like e.g. right-click "Open link in new tab" on the "Get data"/"UCSC main table browser" link in Galaxy. Once UCSC has loaded in the new tab it can be used to send data back to Galaxy without any problems.

HTH

Best wishes, Peter

On 18/11/13 23:03, Jingchao Zhang wrote:
Dear all,

Today I installed the SSL module for our local Galaxy instance and the
"https://"; link is working fine. I added this
"<Location"/">

     RequestHeader  set X-URL-SCHEME https

</Location>"
in our Apache configuration file as instructed in this webpage:
http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy

Here are my problems with SSL:
1. Some build in links like "UCSC Main
<http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-galaxy.unl.edu/tool_runner&tool_id=ucsc_table_direct1&hgta_compressType=none&sendToGalaxy=1&hgta_outputType=bed>
 table
browser" and "UCSC Test
<http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-galaxy.unl.edu/tool_runner&tool_id=ucsc_table_direct_test1&hgta_compressType=none&sendToGalaxy=1&hgta_outputType=bed>
 table
browser" become invalid. If I click on them, nothing will happen, as if
they are blocked.
2. The old "http" link still works, which I think shouldn't because I
added the "RequestHeader ... https" line in Apache configuration. I
really want to disable the http link because the new users could be
easily led to the old one.

Both httpd and Galaxy have been restarted after the changes are made.
Since I didn't find any similar threads in the mailist, I hope someone
here can help me out with this.

Thanks,
Jim


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--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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