galaxy-central and nginx

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galaxy-central and nginx

Jorrit Boekel
Hi all,

I’m testing the latest galaxy-central (rev 15961:63d901ca0e6e) to try out dataset collections. First thing I run into is that things don’t seem to run well when running it on a VM (port forwarded) with nginx. If I click on tools I get a white screen instead of tool options, and the log show an error from lib/galaxy/webapps/galaxy/api/tools.py : Checking parameter file failed.

The setup: URL would be galaxydomain.com:3030, which the VM manager forwards to port 80 on the galaxy VM, which there nginx would forward to port 8080. Now, my nginx is set up to work with older galaxy versions, I don’t know if that matters. I haven’t changed any config files at all yet.

When I turn off nginx and serve directly on port 80 (using sudo), things look like they work. At least the tools look like they should. Has the nginx config to use changed recently or is this some weird artefact? Anyone else seen it? Since I’m just goofing around to see how collections work, it is not the end of the world for me, and I know galaxy-dist is the stable one, but still.

cheers,

Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden



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Re: galaxy-central and nginx

John Chilton-4
On Fri, Jan 9, 2015 at 10:42 AM, Jorrit Boekel
<[hidden email]> wrote:
> Hi all,
>
> I’m testing the latest galaxy-central (rev 15961:63d901ca0e6e) to try out dataset collections. First thing I run into is that things don’t seem to run well when running it on a VM (port forwarded) with nginx. If I click on tools I get a white screen instead of tool options, and the log show an error from lib/galaxy/webapps/galaxy/api/tools.py : Checking parameter file failed.
>
> The setup: URL would be galaxydomain.com:3030, which the VM manager forwards to port 80 on the galaxy VM, which there nginx would forward to port 8080. Now, my nginx is set up to work with older galaxy versions, I don’t know if that matters. I haven’t changed any config files at all yet.
>
> When I turn off nginx and serve directly on port 80 (using sudo), things look like they work. At least the tools look like they should. Has the nginx config to use changed recently or is this some weird artefact? Anyone else seen it? Since I’m just goofing around to see how collections work, it is not the end of the world for me, and I know galaxy-dist is the stable one, but still.

I have not seen this and haven't heard of anyone else - it probably
doesn't have anything to do with -central versus -stable though - I
don't think I have seen any changes related to this recently. Are you
sure you have setup all the same configuration options in your new
Galaxy instance (e.g. nginx_x_archive_files_base,
nginx_x_accel_redirect_base, nginx_upload_store, nginx_upload_path,
remote_user, etc...)? Also do you have the same number of web threads
and handler threads or both instances - if you configured you older
instance to use multiple processes your new instance will need to be
configured to do this as well.

Otherwise I am out of ideas - sorry. Good luck with dataset
collections - there is still a lot of work that needs to be done in
-central for collections for sure but I am really excited about the
potential proteomics applications.

-John


>
> cheers,
> —
> Jorrit Boekel
> Proteomics systems developer
> BILS / Lehtiö lab
> Scilifelab Stockholm, Sweden
>
>
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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Re: galaxy-central and nginx

Jorrit Boekel
I thought the difference may be in the -central config handling that didn’t work with my universe_wsgi anymore or something. Will be hard to trace so I will leave this for now.
I'll mail you more about the collections though, probably tomorrow.

cheers,

Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden



On 15 Jan 2015, at 16:27, John Chilton <[hidden email]> wrote:

> On Fri, Jan 9, 2015 at 10:42 AM, Jorrit Boekel
> <[hidden email]> wrote:
>> Hi all,
>>
>> I’m testing the latest galaxy-central (rev 15961:63d901ca0e6e) to try out dataset collections. First thing I run into is that things don’t seem to run well when running it on a VM (port forwarded) with nginx. If I click on tools I get a white screen instead of tool options, and the log show an error from lib/galaxy/webapps/galaxy/api/tools.py : Checking parameter file failed.
>>
>> The setup: URL would be galaxydomain.com:3030, which the VM manager forwards to port 80 on the galaxy VM, which there nginx would forward to port 8080. Now, my nginx is set up to work with older galaxy versions, I don’t know if that matters. I haven’t changed any config files at all yet.
>>
>> When I turn off nginx and serve directly on port 80 (using sudo), things look like they work. At least the tools look like they should. Has the nginx config to use changed recently or is this some weird artefact? Anyone else seen it? Since I’m just goofing around to see how collections work, it is not the end of the world for me, and I know galaxy-dist is the stable one, but still.
>
> I have not seen this and haven't heard of anyone else - it probably
> doesn't have anything to do with -central versus -stable though - I
> don't think I have seen any changes related to this recently. Are you
> sure you have setup all the same configuration options in your new
> Galaxy instance (e.g. nginx_x_archive_files_base,
> nginx_x_accel_redirect_base, nginx_upload_store, nginx_upload_path,
> remote_user, etc...)? Also do you have the same number of web threads
> and handler threads or both instances - if you configured you older
> instance to use multiple processes your new instance will need to be
> configured to do this as well.
>
> Otherwise I am out of ideas - sorry. Good luck with dataset
> collections - there is still a lot of work that needs to be done in
> -central for collections for sure but I am really excited about the
> potential proteomics applications.
>
> -John
>
>
>>
>> cheers,
>> —
>> Jorrit Boekel
>> Proteomics systems developer
>> BILS / Lehtiö lab
>> Scilifelab Stockholm, Sweden
>>
>>
>>
>> ___________________________________________________________
>> 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:
>>  https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>  http://galaxyproject.org/search/mailinglists/

___________________________________________________________
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:
  https://lists.galaxyproject.org/

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