Running Galaxy tools locally using bx-python

Question

[Thomas]

Hello,

There is a tool on the Galaxy platform which could potentially be very useful for the type of research that I am undertaking. The tool is 'Stitch MAF blocks' which can be found under the 'Fetch Alignments/Sequences' header.

The problem I have is that, because of the size of the data that I would be working with, I would need to try and run the function locally on my own system and using a command line (to enable access to local HPC resources)

I have installed the bx-python library (https://bitbucket.org/james_taylor/bx-python/wiki/Home) on my local system.

I think I am right in saying that these are the set of python scripts which essentially underlie the MAF manipulation tools (as well having many other functions) on the Galaxy platform.

However - the problem I have now - is that looking at all the files contained within the bx-python library - I can't easily discern a clear relationship between the python scripts contained within the library and the particular tool of interest on the Galaxy platform.

As a result, my question is the following:

Which Python files in the bx-python library correspond to the 'Stitch MAF blocks' function on the Galaxy platform?

[Biomonika (Noolean)]

I am thinking Galaxy biostars might be a better fit for your question: https://biostar.usegalaxy.org/

[Thomas]

Thank you, I did not know about this resource

Answer 1

[martenson]

The tool is executing the command defined here:

https://github.com/galaxyproject/galaxy/blob/master/tools/maf/interval_maf_to_merged_fasta.xml#L7-L9

so you are probably looking for file interval_maf_to_merged_fasta.py

[Thomas]

Thank you - this has helped me a lot