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 and 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 Feedback is definitely welcome.



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"<>  wrote:

Hi Dave,

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<>  wrote:
I've essentially asked the same question of the list in the past and gotten no 
real response.

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 cufflinks
* 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 their history
- 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.



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