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?
Question: Running Galaxy tools locally using bx-python
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Thomas Bradley • 90 wrote:
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modified 9 months ago
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3.3 years ago by
Thomas Bradley • 90
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martenson • 380 wrote:
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
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I am thinking Galaxy biostars might be a better fit for your question: https://biostar.usegalaxy.org/
Thank you, I did not know about this resource