Forum:Bioinfor pipeline question

Question

[itshuang]

Hi,

I am new here and like to pose my questions regarding the use of bioinfo pipeline to facilitate analytical workflow. I received user request to automate their analyses of short peptide sequences using several web-based tools (no web service available as yet) and thought about using workflow management system (WMS) to do that. If any of you have experience to tackle this kind of problem before, would you share your view and recommend some WMS or pipeline suitable for this purpose? For scripting, I am considering Python/Jython or Perl to emulate http request/response. Any better ways doing that?

Thanks!

[itshuang]

I found a paper dealing with similar problem: http://www.biomedcentral.com/1471-2105/12/S14/S5

[Devon Ryan]

I look forward to seeing if you get a really good solution to this. Dealing with web-based tools that don't have any sort of stable API is a royal PITA. The only time I've ever done this I've used methods similar to what you outlined.

[itshuang]

Hi, Devon,

I am with you!

Answer 1

[CikLa]

Hi itshuang,

Actually what kind of workflow that you need to do? I prefer using Perl fro scripting and bash script to automate the job. But having a WMS would be nice. Looking forward from answer from the other members as well.

[itshuang]

Hi, CikAlal,

The user wants to use several web-based tools to analyze some sequences sequentially. Result from each step needs to be pre-processed to be the input for the next step. Theoretically, a pipeline should help. But after some initial search, I have not found one that meets my needs. A plain simple way is just to use http request & response to take care of that. Any better idea?