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

Question

[sondeskalboussi]

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

[sridhar56]

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

[sondeskalboussi]

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

[sridhar56]

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

Answer 1

[Ido Tamir]

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/

[sondeskalboussi]

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