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 <bbim...@gmail.com> wrote:
> 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 a
> list of those files. However, the information at this point is text
> (basically a list of filepaths).
> It would be nice to automatically create datasets for those files. Some
> of the time there's a simple 1:1 between file and the user-facing dataset
> (like images); however, for genomes we really want to make a paired
> collection. BioBlend makes it relatively easy to go from filepaths to
> datasets; however, the authentication issue is what wasnt clear.
> If there's a more standard path to go from list of files -> galaxy dataset
> I'm all ears.
> On Wed, Apr 29, 2015 at 12:13 PM, John Chilton <jmchil...@gmail.com>
>> Unofficial way of doing this and the workaround of using configfiles
>> can be found in this thread:
>> 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.
>> On Wed, Apr 29, 2015 at 2:58 PM, Ben Bimber <bbim...@gmail.com> wrote:
>> > Hello,
>> > I am new to galaxy. I"m trying to write a data input tool wrapper. It
>> > call a script that does a query, produces a list of files, and then the
>> > is to use the BioBlend API to create datasets/data collections in
>> > 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
>> > dataset collection in galaxy for each genome.
>> > In theory using bioblend to create datasets is easy. However, when I
>> > this as a galaxy tool, I have not found a clean way to pass the
>> > 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
>> > there's a good change I will find a property with the information I
>> > 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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