Collin Tokheim

icon company Dana-Farber Cancer Institute icon location Boston, MA icon location I am a data scientist that develops machine learning algorithms to gain insight into cancer

Results 3 comments of Collin Tokheim

PyVCF error

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...

Require snvboxGenes.fa file

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),...

Feature request: add continuous integration

@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...