epidisco
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hammerlab
Personalized cancer epitope discovery and peptide vaccine prediction pipeline
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] =...
Currently we have a link to a directory with two MD files and one script (https://github.com/hammerlab/epidisco/blob/master/docs), we should link to the MD file individually (if they are still up to...
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...
Right now we get a "pipeline compile-time error"; we want the error to be clearer and at the level of the CLI parser. ``` epi.ml: internal error, uncaught exception: (Invalid_argument...
STAR OOM
STAR needs memory limit some cases ``` Mar 22 07:03:21 ..... Started sorting BAM EXITING because of fatal ERROR: not enough memory for BAM sorting: SOLUTION: re-run STAR with at...
This is just me thinking out loud while trying to re-run the pipeline for more than 80 patients to get the results from new type(s) of analyses/tools: I think we...
