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Old 07-11-2013, 09:53 AM   #1
moritz1
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Default Which bioinformatic workflow management system to use?

see below..

Last edited by moritz1; 02-25-2016 at 04:45 AM.
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Old 07-11-2013, 10:57 AM   #2
chadn737
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You can install a local instance of galaxy that way you don't have to load it onto their server.
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Old 07-12-2013, 11:02 AM   #3
gene_x
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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..
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Old 02-25-2016, 04:35 AM   #4
Fabien Campagne
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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
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Old 02-26-2016, 04:40 AM   #5
maxsalm
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I can highly recommend Ruffus http://www.ruffus.org.uk/
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