Question: Running Galaxy tools locally using bx-python
gravatar for Thomas
5.0 years ago by
Cambridge, UK
Thomas100 wrote:


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 ( 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?

ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 5.0 years ago by Thomas100

I am thinking Galaxy biostars might be a better fit for your question:

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.0 years ago by Biomonika (Noolean)3.1k

Thank you, I did not know about this resource

ADD REPLYlink written 5.0 years ago by Thomas100
gravatar for martenson
5.0 years ago by
martenson380 wrote:

The tool is executing the command defined here:

so you are probably looking for file

ADD COMMENTlink modified 13 months ago by _r_am32k • written 5.0 years ago by martenson380

Thank you - this has helped me a lot

ADD REPLYlink written 5.0 years ago by Thomas100
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