Hello, I am exploring the possibility of using a local galaxy installation for light bioinformatics on sequence data in the scope of an existing LIMS system. Ideally I would like to be able to do the following 1. Push datasets from the LIMS to galaxy (directly into the user's account or into a fresh temporary session) 2. Allow the user to perform tasks within galaxy, backtracking and retrying as necessary. 3. Push the results along with the galaxy history (ideally converted to a workflow) back to the LIMS 4. (Allow workflows stored in the LIMS to be pushed to Galaxy along with further datasets or even completely automatic launch of these workflows from within the LIMS) Is this feasible? How much wrok would be required? Since I am new to Galaxy (at least from the development side), I would very much appreciate comments advice and pointers to documentation or existing projects of a similar nature. Thanks in advance, Bernhard
Hello Bernhard, I came across your question and see that you may never have had a reply. If you have this already worked out, then great! But if not, perhaps the API wikis will be of interest: http://galaxyproject.org/wiki/Learn/API The documentation is still in progress, but the main points are present and the examples should be helpful. The general idea is that the LIMS system should be able to communicate with Galaxy via the API. If you have specific question about any unresolved issues around LIMS/API integration, please send a brand new question (new email, new thread, new subject) to the galaxy-dev mailing list and we will do our best to offer (quicker!) help. Our sincere apologies for the delayed reply, Best, Jen Galaxy team On 6/22/11 3:51 AM, Sonderegger Bernhard wrote:
Hello,
I am exploring the possibility of using a local galaxy installation for light bioinformatics on sequence data in the scope of an existing LIMS system. Ideally I would like to be able to do the following
1. Push datasets from the LIMS to galaxy (directly into the user's account or into a fresh temporary session) 2. Allow the user to perform tasks within galaxy, backtracking and retrying as necessary. 3. Push the results along with the galaxy history (ideally converted to a workflow) back to the LIMS 4. (Allow workflows stored in the LIMS to be pushed to Galaxy along with further datasets or even completely automatic launch of these workflows from within the LIMS)
Is this feasible? How much wrok would be required?
Since I am new to Galaxy (at least from the development side), I would very much appreciate comments advice and pointers to documentation or existing projects of a similar nature.
Thanks in advance,
Bernhard
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participants (2)
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Jennifer Jackson -
Sonderegger Bernhard