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How to run Galaxy pipeline using a python code (is there a module, package for galaxy tools)

Hello, am new in NGS data analysis and i was wondering if i can write a python script to perform the different steps of Galaxy pipeline, in other words, is there command lines, package or modules that i can call within my script. Thanks in advance

genome sequencing assembly
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updated by Ido Tamir Ido Tamir • written by sondeskalboussi • sondeskalboussi

If you write a xml file in the Galaxy format, it should do the task

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written by sridhar56 sridhar56

Hi, am not a computer scientist so have no idea about xml files

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written by sondeskalboussi • sondeskalboussi

Actually if you can write a Python script, writing xml files should be may more easier.

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written by sridhar56 sridhar56

1 answer

Look at bioblend: http://bioblend.readthedocs.io/en/latest/api_docs/galaxy/docs.html it wraps galaxys REST API Ask more questions at: https://biostar.usegalaxy.org/

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written by Ido Tamir Ido Tamir

Thank you Ido, am gonna start diving on it, thanks for ur help

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written by sondeskalboussi • sondeskalboussi

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