Julia Kodysh

These should correspond to what we actually have in prod.

netmhc-3.4 silently drops predictions

6

Using `netmhccons` results in these errors, which come from `netmhc-3.4`: ``` Traceback (most recent call last): File "/Users/julia/code/netmhc-bundle/netMHC-3.4/netMHC.py", line 535, in main() File "/Users/julia/code/netmhc-bundle/netMHC-3.4/netMHC.py", line 522, in main preds[entry] =...

Would be great to have something similar to https://github.com/hammerlab/epidisco/blob/master/docs/running-on-coclobas.md but for Secotrec. Also would be very helpful to add info about how to run multiple samples, similar to the batch...

Installing igvxml.0.0.6 fails in test example

1

I ran a slightly modified test example: ``` source configuration.env KETREW_CONFIGURATION=_kclient_config/configuration.ml; DREAM=https://storage.googleapis.com/dream-challenge; ocaml run_pipeline.ml pipeline \ --normal $DREAM/synthetic.challenge.set2.normal.bam \ --tumor $DREAM/synthetic.challenge.set2.tumor.bam \ --reference-build hg38 \ --mouse-run \ --with-mutect2 \ --results-path...