[galaxy-dev] galaxy with torque

Hello all, My name is Edgar Fernandez. I'm a sys. admin. at University of Montreal. I've contacted you a while back about installing galaxy and I've successfully done it on a redhat 6 server. I see myself in a situation where I need to utilise all my redhat servers (who are identical to the ser

Re: [galaxy-dev] master_api_key currently doesn't benefit from a real admin's key?!

Ok, I'll figure out what I can take on here in terms of being more systematic about determining the various error cases/fixes visa vis the master_api_key and the API, and will get back to you. Having the master key work without a user object does sound like the pure way to go. Thanks, d. ___

Re: [galaxy-dev] Unable to add tools from tool shed

The tutorial uses bwa_base from the Test ToolShed which is not on Main, however I just tested bwa_mem from the Main ToolShed and it installed correctly. Please send us more information about the error you are encountering. In the Manage installed tool shed repositories

Re: [galaxy-dev] master_api_key currently doesn't benefit from a real admin's key?!

Thanks for the detailed description - this gives me a better understanding of what is going on. Okay - I think the right way to handle this is probably to make the master api key work everywhere where the user API key is insufficient. It makes sense to me that the master API key for instance canno

Re: [galaxy-dev] Unable to add tools from tool shed

Is there a actually a "Repository Installation Error below" - it is hard to say what went wrong without more logging? It is certainly frustrating that that package installation is failing - it seems to be a quite straight-forward installation definition. -John On Thu, Nov 13, 2014 at 3:19 PM, Ry

Re: [galaxy-dev] Creation of a backup/migrate script for data/users

This is a tough question - I suspect it will be difficult no matter how you proceed. The API objects don't map 100% directly to database objects and may not have complete coverage - but using the database directly will require one to learn a lot of Galaxy's data model I suspect. A middle ground -

Re: [galaxy-dev] Problem with LWR (input size limitation)

On Wed, Nov 19, 2014 at 12:58 PM, Misharl Monsoor wrote: > Hi John , > > First all, thank you very much for your quick reply. I will test your > suggestion about pycurl, and tell you if it has worked. For the second > question, i was wondering if it is possible with LWR to define a path (where >

Re: [galaxy-dev] Fw: Re: galaxy server file upload problem

Johngui, Right, what Sam also asked for is the URL I'd want to see to know where things are going wrong. One other note: In your screenshots in the powerpoint deck it looks like you're accessing galaxy directly on port 8080 instead of going through nginx, which is listening on 80. Can you try h

Re: [galaxy-dev] Fw: Re: galaxy server file upload problem

Hi Johngui, Can you open the console in your web browser and look at the url to which the file was posted to? Also please take a look into the Galaxy configuration file (config/galaxy.ini or universe_wsgi.ini) and try to find out to what the nginx_upload_path is set to. Thanks, Sam On Wed, Nov

Re: [galaxy-dev] rename output dataset in workflow - input dataset variable

Yes :( There's been some past discussion of this from a tool developer perspective, e.g. https://trello.com/c/JnhOEqow and http://dev.list.galaxyproject.org/Using-input-dataset-names-in-output-dataset-names-td4662481.html The best individual tool authors can do is something like "$input.name proc