Which bioinformatic workflow management system to use?

[moritz1]

see below..

[chadn737]

You can install a local instance of galaxy that way you don't have to load it onto their server.

[gene_x]

I have tried Bpipe and it seems to work well. It takes some time to learn and get used to its way of doing things.

You can also write a shell script and I find it to be easier to understand..

But if your users will be doctors who might not have any unix experience. Anything that has a web interface will be much easier to use than unix environment..

[Fabien Campagne]

I realize you are likely done with your thesis, so this information is for those who may stumble upon this thread. I would suggest to take a look at the latest development: NextflowWorkbench. Here's a preprint that discusses this new workflow system:

NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts
Jason P Kurs, Manuele Simi, Fabien Campagne
bioRxiv doi: http://dx.doi.org/10.1101/041236

[maxsalm]

I can highly recommend Ruffus http://www.ruffus.org.uk/