The bioBakery help forum

Hallagram does not work

I am a biomedical engineering student and I am currently doing a project where I am going to use HAllA. I downloaded the tool and ran the example: “halla -X X_16_100.txt -Y Y_16_100.txt --output synthetic_output” as given on https://bitbucket.org/biobakery/biobakery/wiki/halla. I also wanted the hallagram, so I ran “cd synthetic_output” and “hallagram similarity_table.txt hypotheses_tree.txt associations.txt --outfile hallagram.png”. Though I did not get the expected plot. I am hoping that you can help me. I am running the tool in Anaconda prompt in Windows 10. The output stated that there was some kind of indexerror, so I attached a screenshot of it.

I hope someone can help me.

Hello Joan, Thank you for all the information! HAllA was developed and tested on Linux and Mac OS. If you could possibly run in docker on Windows I think it should resolve the errors you are seeing.

Thank you,
Lauren