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-us.... There is a Trello card outlining platform work that should be done to support this better but we have not made progress on that. I would be interested in your use case. One can dynamically discover datasets with various db keys and build collections composted of dynamically discovered datasets and keys - but there is no way to use the tool xml to dynamically discover a variable number of collections - but it should be supported - as should building a list of paired or lists of lists where the outer list describes the key and the inner the sample. -John On Wed, Apr 29, 2015 at 2:58 PM, Ben Bimber <bbimber@gmail.com> wrote:
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 of this file, rather than making a dataset from that file. In my case this file has a pair of columns representing FASTQ files, and I want to create one paired dataset collection in galaxy for each genome.
In theory using bioblend to create datasets is easy. However, when I call this as a galaxy tool, I have not found a clean way to pass the credentials to bioblend. BioBlend needs to know the serverURL and either the user's API key or username/password. I think if I poke around $__app__ or $__user__ there's a good change I will find a property with the information I need; however, this has the obvious problem of writing the API key to the log.
Is there another way to approach this problem?
Thanks in advance for any help, Ben
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