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andrewrech / antigen.garnish

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mkdir: cannot create directory ‘/scratch’: Permission denied #120

Closed itamuria closed 4 years ago

itamuria commented 4 years ago

Dear developer,

I am trying to run the first example of the website:

library(magrittr) library(data.table) library(antigen.garnish) dir <- system.file(package = "antigen.garnish") %>% file.path(., "extdata/testdata") dt0 <- "antigen.garnish_example.vcf" %>% file.path(dir, .) %>% garnish_variants %>% .[, MHC := c("HLA-A*01:47 HLA-A*02:01 HLA-DRB1*14:67")] %>% garnish_affinity2

and I am obtaining the next error: Running netMHC in parallel mkdir: cannot create directory ‘/scratch’: Permission denied

How could I give writing permission to netMHC? Thanks, All the best, Ibon

leeprichman commented 4 years ago

Hi Ibon,

This appears to be netMHC trying to create temporary folders for itself, not any of our code being executed. As indicated in the README, antigen.garnish requires sudo permissions to install and execute. Ideally you will need to get administrator privileges or be the root user on your system. You should also make sure the home directory is set to one that you have full permissions for.

If you need an alternative solution, you can visit the wiki for instructions on how to use antigen.garnish with Docker and Amazon Web Services.

leeprichman commented 4 years ago

Hi Ibon,

I hope you were able to resolve this issue! I'm going to close this soon if you don't have any further questions.