Docker Image Created

[obedaram]

This is not an issue with the program, but I wanted to let you know that I created a docker obedaram/snp2hla_um:latest based on your pipeline. I needed to run it in an environment that restricted the use of CSH. I edited the scripts to call the binaries from the docker itself. I disabled the requirements check temporarily. For this docker, the input files need to have the data prefix, I might be able to edit the script in the future to remove it (since you mount it into the docker data folder). I did test all your input files for make references and snp2hla_um.

Please let me know if you have any questions.

Best,

Obed

docker run -v /path/to/data:/data snp2hla_um:latest
MakeReference_UM.csh
/data/HAPMAP_CEU_hg19
/data/HAPMAP_CEU_HLA_new.ped
/data/HAPMAP_CEU_hg19_REF
plink
hg19
5
15
4
10
20
/data/plink.chr6.GRCh37.map \

MakeReference_hg19.log

docker run -v /path/to/data:/data snp2hla_um:latest
SNP2HLA_UM.csh
/data/1958BC_hg38
/data/HAPMAP_CEU_hg38_REF
/data/1958BC_hg38_imputed
plink
5
15
4
10
20
/data/plink.chr6.GRCh38.map \

SNP2HLA_hg38.log