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Old 06-26-2013, 03:27 AM   #1
rdeborja
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Default Data Pipeline Automation, what are you using?

I'm curious to know what type of pipeline workflow automation tool people are using these days. At the start of my career, I started cobbling together various shell scripts which quickly turned into an administrative nightmare. Since then, our institute has implemented SeqWare to perform FASTQ file generation, data QC, alignment and some post-processing.

It would be nice to know what others are using and some of their experiences.
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Old 06-26-2013, 03:45 AM   #2
RickBioinf
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I prefer to make my own pipeline workflow, so I know exactly what the code is and I can change everything. But when it's really necessary I like to use Galaxy.
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Old 06-26-2013, 03:52 AM   #3
rhinoceros
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Lots of pipes in shell scripts.
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Old 06-26-2013, 04:23 AM   #4
maasha
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Biopieces -> www.biopieces.org
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Old 06-26-2013, 04:44 AM   #5
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Quote:
Originally Posted by maasha View Post
Biopieces -> www.biopieces.org
That's in essence how I construct my pipelines, except that I have individually added all the algorithms to my path. So, for example, instead of 'align_pair_seq' I'd use 'muscle' or 'clustal' or whatever does IMO the best job for the given task..
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Old 06-26-2013, 06:50 AM   #6
dpryan
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Bash scripts and the queuing system on our cluster.
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Old 06-27-2013, 10:09 AM   #7
asiangg
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Does anyone use GNU makefiles?
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Old 06-27-2013, 04:44 PM   #8
sdriscoll
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bash, perl, python and C.
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Old 06-27-2013, 04:51 PM   #9
rdeborja
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Quote:
Originally Posted by asiangg View Post
Does anyone use GNU makefiles?
I'm a huge fan of makefiles as a very basic workflow system, especially since it works well with sge's qmake.
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