Collin Tokheim

I think it is related to the setuptools version. I had a user report a similar error for another repo, and changing the setuptools version fixed the installation issue. See...

Hi. The snvboxGenes.fa file (i.e. input of -i in mut_annotate) is generated from the extract_gene_seq command (see https://probabilistic2020.readthedocs.io/en/latest/tutorial.html#gene-fasta). One just needs to download the hg19 fasta file from UCSC (http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit),...

@RachelKarchin I previously added continuous integration (Travis CI) to some of my repositories (e.g., https://github.com/KarchinLab/probabilistic2020). So I believe once it is setup for mhcnuggets, then we just need to toggle...

Ideally one would train an entire new model where silent mutations were not included to then apply it on additional data where they also weren't included. In general, scores will...

This indicates that command line tools from the probabilistic2020 python package could not be found in your PATH environment variable. There are two possibilities: 1) the probabilistic2020 python package is...

Maybe there is an issue because mut_annotate is in your "base" conda environment and not within the 2020plus conda environment. Could you check the bin folder for the 2020plus conda...

Thanks for reporting the issue. Could you provide the exact command that you executed and your python version?

You need to install scikit-learn, which was listed as one of the dependencies in the conda environment yaml file

You need to install the correct version of scikit learn, which is already specified in the conda environment file (scikit-learn

This seems like it may be a path error to where the 2020plus_10k.Rdata is located, and therefore R throws an error. I suspect if you put the full path to...