Re: [galaxy-dev] Authenticating Against Galaxy from within a tool?

2015-04-29 Thread Ben Bimber
John - thanks, your configfile example should work for API key. however, is there a cheetah substitution to pull in the server's URL? On Wed, Apr 29, 2015 at 12:20 PM, Ben Bimber wrote: > Hi John, > > Thanks. To elaborate a little more: we have a LabKey Server (web front > end for a databa

Re: [galaxy-dev] Authenticating Against Galaxy from within a tool?

2015-04-29 Thread Ben Bimber
Hi John, Thanks. To elaborate a little more: we have a LabKey Server (web front end for a database) that manages raw files and metadata. The idea is to make a galaxy tool where a user could do thing like query for all genomes from males patients, age x-y, etc. I can use LabKey's APIs to return

Re: [galaxy-dev] Authenticating Against Galaxy from within a tool?

2015-04-29 Thread John Chilton
Unofficial way of doing this and the workaround of using configfiles can be found in this thread: http://dev.list.galaxyproject.org/Simple-standard-for-API-use-of-a-global-user-key-that-all-loaded-tools-can-draw-upon-td4665659.html. There is a Trello card outlining platform work that should be done

[galaxy-dev] Authenticating Against Galaxy from within a tool?

2015-04-29 Thread Ben Bimber
Hello, I am new to galaxy. I"m trying to write a data input tool wrapper. It will call a script that does a query, produces a list of files, and then the plan is to use the BioBlend API to create datasets/data collections in galaxy. In other words I am making the dataset(s) based on the contents