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
Is there another way to approach this problem?
Thanks in advance for any help,
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