at InterMine we are looking to improve various aspects of our UI, and
also our interaction with Galaxy. To that end, it would be great to find
out what ways there are of depositing data in a user's account. The
another tab, or can be entirely backgrounded.
After some reading of the bitbucket repos I note that:
a) I can use the current mechanism of a data_source.py tool such as
the flymine et al. ones. This would require me to do things like
parsing the response headers for the galaxy session though, and I
don't see a nice way of depositing data in a user's account without
having come originally from galaxy.
b) The API provides mechanisms for associating data files with
histories, provided that these files have been already uploaded.
It is straightforward to operate on a specific account, but I didn't
find the API controller that allows individual tools, rather than
whole workflows to be run. This would be ok I guess if I could
create workflows rather than just run them.
So the current situation (please correct me if I am mistaken) is a
web-app based workflow that is best originated in galaxy, and an API
workflow that lacks certain features to do what I'd like. Again, I'd
very much like to be wrong here, and have like just not connected the
However, if that is an accurate summation of the situation, I would be
happy to contribute to get what I want, rather than expecting others to
provide it. If anyone is interested in pull requests and a few questions
about internals, I'd be happy to help develop the API so that:
a) POST /workflows -> creates a new workflow (from one or more tools),
rather than running it.
b) GET /jobs -> lists the status of running or completed jobs.
c) POST /jobs -> runs a job (from a workflow), returning a job id.
d) DELETE /jobs -> cancels a job, or removes it from the history
University of Cambridge
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