Unable to download netMHC data tar from DTU.

[nickhir]

Hello, I am using docker to run antigen.garnish and I think everything worked as intended so far. However, when I run

# predict neoantigens
result <- dt %>% garnish_affinity(.)

I get the following error: Error in FUN(X[[i]], ...) : Unable to download netMHC data tar from DTU. I looked into the source code and saw the function is trying to download something from here: link <- "http://www.cbs.dtu.dk/services/NetMHC-4.0/data.tar.gz". I have the suspicion that the data.tar.gz was moved to a different URL.

Do you think this might be the case or am I missing something else?

Cheers!

[andrewrech]

Hi Nick,

Yes, I think you're right. Here are the new data links. I will re-build the Docker image and upload when I have a moment in the next few days.

"https://services.healthtech.dtu.dk/services/NetMHC-4.0/data.tar.gz"
"https://services.healthtech.dtu.dk/services/NetMHCII-2.3/data.Linux.tar.gz"
"https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/data.tar.gz"
"https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/data.tar.gz"

[nickhir]

Thank you very much for your quick responds! It is really appreciated. I would really like to try antigen.garnish right away.
I thought if I manually update the paths in /root/src/R/antigen.garnish_run.R everything should work, but I still get the same error.. Could you maybe tell me which file I have to update so the download works?

I will re-download the docker image as soon as you have the time to re-build it

[andrewrech]

Hi Nick,

After you update the paths, navigate to the top-level directory and re-install:

cd /root/src
R CMD INSTALL .

You could also update this function, source it in the global environment, and then run from the data directory, which by default is ~/antigen.garnish:

https://github.com/andrewrech/antigen.garnish/blob/2ceffdfbc42e1ba57639859e9ee9bcab4c38d4e7/R/antigen.garnish_run.R#L205-L331

[nickhir]

Sorry to bother you again. The first two downloads now work, but the third one has the wrong URL I think (https://services.healthtech.dtu.dk/services/NetMHCIIpan/data.tar.gz).

Is it maybe this one instead? https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/data.tar.gz

[andrewrech]

Whoops. Yes.

[nickhir]

Thank you very much! Everything works as intended now as far as I can tell. Just as a side note, I don't think it is to important, but list_mhc() does not work for me. It doesnt return anything.

[leeprichman]

I’ve seen this happen when R doesn’t feel like printing too many lines sometimes. Try forcing it with print(list_mhc()) and let us know if that fixes it.

[nickhir]

Unfortunately there is still no output.

[andrewrech]

> library(antigen.garnish)
> dt <- list_mhc()
> str(dt)
Classes ‘data.table’ and 'data.frame':  16701 obs. of  3 variables:
 $ MHC    : chr  "DRB1_0101" "DRB1_0103" "DRB1_0301" "DRB1_0401" ...
 $ species: chr  "human" "human" "human" "human" ...
 $ class  : chr  "II" "II" "II" "II" ...
 - attr(*, ".internal.selfref")=<externalptr>

data.table returns invisibly by default - save the table to an object

[nickhir]

Nice! Now I can see them all.

[andrewrech]

https://github.com/andrewrech/antigen.garnish/commit/2a870a1c68380ef5fcec5a23939dd343f89be4b0