Running toolshed on localhost is broken in release_17.09?

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Running toolshed on localhost is broken in release_17.09?

Peter Briggs
Hello

I'm trying to run a toolshed instance on localhost to test some local tool changes - this works okay in release_17.05, but setting one up using release_17.09 appears to be broken out of the box, at least for me.

In release_17.09, after configuration connecting to http://127.0.0.1:9009/ brings up a version which isn't usable - the styles are missing and it it's not possible to navigate, register/login etc.

Uncommenting lines like

  # Serving static files (needed if running standalone)
  static_enabled: True

in the config/tool_shed.yml file don't seem to make any difference.

I didn't find anything in the Galaxy Github issue list about this, so has anyone else observed this behaviour? For now I've just gone back to release_17.05 for my local toolshed needs.

Thanks

Peter

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Re: Running toolshed on localhost is broken in release_17.09?

Nate Coraor (nate@bx.psu.edu)
Hi Peter,

This might be due to the switch from Paste to uWSGI for reports and tool shed applications in 17.09. I do see that when using the 17.09 default configuration (uWSGI with config/tool_shed.yml.sample), the static content is not configured to be served, so I submitted a fix for that here:


However, if you have an existing tool_shed.ini, run_tool_shed.sh is supposed to continue to use Paste, and since run_tool_shed.sh (presumably) decided to start with uWSGI instead of Paste, it did not find your tool_shed.ini. Is it located somewhere other than config/tool_shed.ini?

--nate

On Wed, Feb 14, 2018 at 9:34 AM, Peter Briggs <[hidden email]> wrote:
Hello

I'm trying to run a toolshed instance on localhost to test some local tool changes - this works okay in release_17.05, but setting one up using release_17.09 appears to be broken out of the box, at least for me.

In release_17.09, after configuration connecting to http://127.0.0.1:9009/ brings up a version which isn't usable - the styles are missing and it it's not possible to navigate, register/login etc.

Uncommenting lines like

  # Serving static files (needed if running standalone)
  static_enabled: True

in the config/tool_shed.yml file don't seem to make any difference.

I didn't find anything in the Galaxy Github issue list about this, so has anyone else observed this behaviour? For now I've just gone back to release_17.05 for my local toolshed needs.

Thanks

Peter

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

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Re: Running toolshed on localhost is broken in release_17.09?

Peter Briggs
Hello Nate

Thanks for looking into this so quickly - I've manually applied the patch in your PR for toolshed.yml.sample and that works perfectly, thanks!

Re picking up older .ini config files for a toolshed instance: what I was doing was spinning up a completely new pair of Galaxy and toolshed instances on my local machine, just for testing purposes. So in this case there was no pre-existing .ini files to be picked up.

Hope that makes sense - thanks again for your help, and the patch.

Best wishes

Peter

-- 
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482


From: Nate Coraor [[hidden email]]
Sent: Wednesday, February 14, 2018 4:19 PM
To: Peter Briggs
Cc: [hidden email]
Subject: Re: [galaxy-dev] Running toolshed on localhost is broken in release_17.09?

Hi Peter,

This might be due to the switch from Paste to uWSGI for reports and tool shed applications in 17.09. I do see that when using the 17.09 default configuration (uWSGI with config/tool_shed.yml.sample), the static content is not configured to be served, so I submitted a fix for that here:


However, if you have an existing tool_shed.ini, run_tool_shed.sh is supposed to continue to use Paste, and since run_tool_shed.sh (presumably) decided to start with uWSGI instead of Paste, it did not find your tool_shed.ini. Is it located somewhere other than config/tool_shed.ini?

--nate

On Wed, Feb 14, 2018 at 9:34 AM, Peter Briggs <[hidden email]> wrote:
Hello

I'm trying to run a toolshed instance on localhost to test some local tool changes - this works okay in release_17.05, but setting one up using release_17.09 appears to be broken out of the box, at least for me.

In release_17.09, after configuration connecting to http://127.0.0.1:9009/ brings up a version which isn't usable - the styles are missing and it it's not possible to navigate, register/login etc.

Uncommenting lines like

  # Serving static files (needed if running standalone)
  static_enabled: True

in the config/tool_shed.yml file don't seem to make any difference.

I didn't find anything in the Galaxy Github issue list about this, so has anyone else observed this behaviour? For now I've just gone back to release_17.05 for my local toolshed needs.

Thanks

Peter

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

___________________________________________________________
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:
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___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/