You are correct in that, so far, there isn't any formal documentation of
the API, and it should still be considered a beta feature. There is a
workflow API, and the best way to see how it works right now is, like
you mentioned, browsing the scripts/api directory for usage examples or
reading the api source itself. The two relevant sample scripts for
workflows are workflow_execute.py and example_watch_folder.py for a more
involved demo that uploads files from a regular system folder to a data
library within galaxy, and then executes a workflow on them.
As Pieter mentioned earlier in the thread, we made significant progress
towards addressing this within the standard galaxy UI at the recent
hackathon, and it has been committed to galaxy-central. Depending on
your needs, you might not need to use the API at all. If you'd like to
give it a try, the relevant changeset in galaxy-central is
5385:b9cff3fbd170, which is also on test.g2.bx.psu.edu
. Feedback is
On 04/18/2011 10:56 AM, Dave Walton wrote:
As far as I can tell there are no real docs for the API. The best I’ve been able to
find is what’s under the scripts/api directory. I believe the API is still considered a
“beta” at best.
Galaxy team, are there any updates on the API, documentation plans, etc?
On 4/15/11 1:14 PM, "Leandro Hermida"<softdev(a)leandrohermida.com>
Thanks for the feedback, this to me would be a very useful feature to be able to spawn
multiple same jobs or workflows from one tool form using different input datasets selected
with multi select and all other form parameters being the same.
Where are the docs and information for the Galaxy API? Wondering if I could program this
exact functionality in the script that the tool would execute.
On Fri, Apr 15, 2011 at 4:28 PM, Dave Walton<Dave.Walton(a)jax.org> wrote:
I've essentially asked the same question of the list in the past and gotten no real
I have the same interest, but from a workflow perspective.
* A module that allows me to select multiple datafiles (say fastq files)
* Then pass each data file to a separate instance of a workflow that runs tophat and
* then another module that takes the final outputs of each of the workflow runs and sends
them to a final module that merges results.
I am attempting to implement something like this using the API, though the API is still
pretty green from my perspective.
I think functionality like this built into the workflow editor would be a great
On Apr 15, 2011, at 8:14 AM, Leandro Hermida wrote:
> Hi everyone,
> I was wondering what would be the way in Galaxy to program the following:
> - User clicks on a tool and form is displayed
> - They use a select multi menu in the form to pick lets say X multiple datasets from
> - When they click submit the tool launches X number of jobs in the history, on for
each of the datasets selected.
> I have a common use case where users have to manually run the same tool over and over
again with the same parameters for each dataset of interest in their history. I would be
great to be able programmatically or otherwise with Galaxy to be able to use one form and
multi select the datasets and then launch the parallel jobs in one go.