Hi Nate,

Thanks so much for the help.

Aslo, I solved my second issue. Here are the the changes I made to the Apache 
conf file.
RewriteCond %{HTTPS} off
#RewriteRule ^(.*) http://localhost:8080$1 [P]
RewriteRule ^/?(.*) https://%{SERVER_NAME}/$1 [R,L]
Now http will be redirected to https. Just put it here for future reference in 
case anyone needs to know.

Best,
Jim

________________________________
From: Nate Coraor <n...@bx.psu.edu>
Sent: Tuesday, November 19, 2013 1:14 PM
To: Jingchao Zhang
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] secure Galaxy with SSL

On Tue, Nov 19, 2013 at 12:32 PM, Jingchao Zhang 
<zh...@unl.edu<mailto:zh...@unl.edu>> wrote:
Hi Peter,

Thanks so much for your help! It is like you said a browser issue.

I also noticed that the Galaxy main server (https://usegalaxy.org/) doesn't 
have this problem. And their USCS main table browser uses "https" instead of 
"http". Does anyone know why this isn't included in the current Galaxy release? 
And how can I change my current "http USCS main" to "https USCS main"?

Hi Jim,

We did this for usegalaxy.org<http://usegalaxy.org> simply by locally changing 
the URL in the tool's config from http to https.  A proper fix for this tool 
(and other external sites which open in the center iframe) is in the works and 
will be released to the stable branch once it's done.

--nate


Thanks,
Jim


Message: 8
Date: Tue, 19 Nov 2013 08:51:03 +0000
From: Peter Briggs 
<peter.bri...@manchester.ac.uk<mailto:peter.bri...@manchester.ac.uk>>
To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] secure Galaxy with SSL
Message-ID: 
<528b2677.9050...@manchester.ac.uk<mailto:528b2677.9050...@manchester.ac.uk>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

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<mailto:peter.bri...@manchester.ac.uk>
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
___________________________________________________________
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To search Galaxy mailing lists use the unified search at:
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___________________________________________________________
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