4.3 years ago by
United States
This sounds like the exact kind of workflows dataset collections (http://bit.ly/gcc2014workflows) included with the latest couple releases of Galaxy have designed to addressed. These features are still need a lot of polish and probably bug fixes - but in theory you should be able to create a workflows that operates over any number of samples in the first several steps and merges them down in the CuffDiff/CuffMerge steps. This would require some modifications to the CuffDiff and CuffMerge tools - hopefully many other tools in the workflow would not need to be modified. I could send you the modifications for the CuffMerge - CuffDiff is a bit trickier - is this a couple conditions with many replicates - or many replicates - or what? If you have a fully expanded version of the workflow with the 80 inputs or a smaller representative workflow with a few I could potentially extrapolate what a modified CuffDiff tool would need to look like (and let you know if I see any other potential pitfalls).
Eventually these tools need to be updated in the tool shed as well - if we get them working well for you - I can try to work on getting whatever changes we make into the tool shed.
Alternatively - what many people have traditionally done to do this kind of work in Galaxy is just to stop the workflow before the CuffDiff/CuffMerge step and run the 80 copies of the simpler workflow (using the batch workflow submission button - let me know if you need more information on that) and then do the merge and diff steps as simple tool executions and then run another workflow for the post-merge analysis.
