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andrewrech / antigen.garnish

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Error: unset environmental variable for antigen.garnish data directory #140

Closed ARChakravarthy closed 3 years ago

ARChakravarthy commented 3 years ago

I've been running tests of the latest version on R 4.1.0 using the inbuilt examples.

library(magrittr) library(data.table) library(antigen.garnish)

load an example VCF

dir <- system.file(package = "antigen.garnish") %>% file.path(., "extdata/testdata")

file <- file.path(dir, "TUMOR.vcf")

extract variants

dt <- garnish_variants(file)

add space separated MHC types

see list_mhc() for nomenclature of supported alleles

MHC may also be set to "all_human" or "all_mouse" to use all supported alleles

dt[, MHC := c("HLA-A01:47 HLA-A02:01 HLA-DRB1*14:67")]

predict neoantigens

result <- dt %>% garnish_affinity(.)

Console output when function breaks

Generating metadata. Reading local transcript metadata. Environmental variable AG_DATA_DIR for the antigen.garnish data directory is unset. Checking standard directories. Error in Sys.setenv(AG_DATA_DIR = ag_dir) : object 'ag_dir' not found Removing temporary files.

andrewrech commented 3 years ago

Thanks for your message. I'm happy to help you get this working.

It appears that the external (to R) dependencies are not installed correctly. Could you provide a reproducible example of how you installed the package and additional information about your system and R environment?

I recommend using the Docker image we provide if possible, which will avoid these issues. Are you able to try Docker?

ARChakravarthy commented 3 years ago

Thank you for your help, appreciate it greatly!

The installation is being handled by IT support on an institutional HPC so I am afraid I don't have access to the installation scripts they are using directly.

If you point me to a relative path tree for the folder structure of the external dependencies I think it would be most illuminating.

andrewrech commented 3 years ago

Hi,

This error message indicates that the installation instructions haven't been followed correctly, so I'm afraid I can't point you to where these files have been installed.

Thanks

ARChakravarthy commented 3 years ago

I have asked IT for a copy of the installation script they used, I will update you once I have it. And also I meant where all the dependencies should be installed or which exact path variables should point to which folders.

Should AG_DATA_DIR be the extdata folder?

ARChakravarthy commented 3 years ago

Turns out they messed up the installation of the dependencies. Closing the issue.