Passing The Url For Ucsc Browser (Send Output To Galaxy)

Question: Passing The Url For Ucsc Browser (Send Output To Galaxy)

7.1 years ago by

Hi, we are running distinct instances on 80 and 8080 - when you use the 8080 instance - the url is built for /galaxy not :8080/galaxy http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=http%3A//genome.ein stein.yu.edu/galaxy/tool_runner&tool_id=ucs thus you cannot pass the data back to the correct instance. What/where is the easiest to pass the 8080 information to the browser? Looking at some candidate files: ucsc_proxy.py ucsc_tablebrowser.xml but perhaps there is a better way, best, joe

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modified 24 months ago by Inquirer • 80 • written 7.1 years ago by Joseph Hargitai • 170

Hi,

I am aware that this is an old question, but I am experiencing exactly the same issue: Galaxy is running on http://address:8080/galaxy, but outputs from "Get Data" tools are sent to http://address/galaxy/tool_runner, which obviously does not exist. Note that it does not only happen with UCSC, but with any other external source of data.

I have been carefully reviewing that NGINX.conf and the Galaxy.ini files, to no avail. Any ideas? Thanks a lot!

EDIT: I have published my answer below!

ADD REPLY • link written 24 months ago by Inquirer • 80

24 months ago by

Inquirer • 80

Inquirer • 80 wrote:

Hi! I originally published a message on this thread explaining that I had come across the same obstacle - upon realizing that it was wrongly posted as an answer, I moved it to the comments section.

Instead, I am now sharing what I did to solve the problem, which I hope can be of use for any Galaxy user that happens to bump into the same. Namely, you only need to open your NGINX configuration file (probably in /etc/nginx/nginx.conf) and there make some changes to your server block.

Before I had the following, based on the instructions from https://wiki.galaxyproject.org/Admin/Config/nginxProxy:

        location /galaxy {
            proxy_pass http://galaxy_app;                                                                   
            proxy_set_header X-Forwarded-Host $host;
            proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        }

I simply changed X-Forwarded-Host $host to X-Forwarded-Host $host:8080 and it started to work fine. I have not tested it thoroughly, but to my understanding now external tools should be aware of the exact URL they should generate.

Please correct if I am mistaken!

ADD COMMENT • link modified 24 months ago • written 24 months ago by Inquirer • 80

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