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Pull Cmd: docker pull edgreen/seq2hla:latest

Run Cmd: docker run -i -t -v /path/to/file/dir/:/workspace/ edgreen/seq2hla -e inputBAM=xx -e threadsN

inputBAM is the file name, e.g. for a file foo.BAM inputBAM=foo
threadN is the number of CPU threads to use for bowtie

Docker Pull Command