Open anoronh4 opened 3 years ago
I agree with this solution. Let's ask @cband and then proceed
One thing need to be noticed is that Neoantigen is before SomaticFacetsAnnotation
, so changing this will result all the maf to be regenerated, although most of them will remain unchanged.
For the question, do you mean this? https://github.com/mskcc/tempo/blob/5c15fc506edbe77479f07999b7035adbc10efe73/containers/neoantigen/Dockerfile#L6-L7
I agree with this solution. Let's ask @cband and then proceed
One thing need to be noticed is that Neoantigen is before
SomaticFacetsAnnotation
, so changing this will result all the maf to be regenerated, although most of them will remain unchanged.For the question, do you mean this? https://github.com/mskcc/tempo/blob/5c15fc506edbe77479f07999b7035adbc10efe73/containers/neoantigen/Dockerfile#L6-L7
yes, i do mean the lines you highlighted. i'm comparing them to the config file for non-docker runs edited here. i'm not sure if 4.0a is older or newer than 4.0. i would have to change neoantigen-docker.config
as well as our docker file.
yes, i do mean the lines you highlighted. i'm comparing them to the config file for non-docker runs edited here. i'm not sure if 4.0a is older or newer than 4.0. i would have to change neoantigen-docker.config as well as our docker file.
Would you mind to check in the docker container if these binary is actually 4.0a
by running: /usr/local/bin/netMHC-4.0/netMHC
and /usr/local/bin/netMHCpan-4.0/netMHCpan
, just to make sure.
I think it's good to go now. You can merge it into master and make the release from master instead of from bugfix/HGVSc_stringparse
Addressing error mentioned in #7 Also changing the
neoantigen-docker.config
file in order to include updated terms used in the newest version ofneoantigen.py
. Question: i noticed that in the default config file the algorithm versions are changed to 4.0 and 4.1b, should we match the docker config?