reproduce_setup/pgx-main/pgx_update.sh

#!/bin/bash

comm -13 <(aws s3 ls s3://quantgene-portland-pgx/ --summarize --human-readable --recursive | awk '{print $5}' | egrep '\.json$' | sed 's/.json$//' | sort) <(aws s3 ls s3://quantgene-portland-pgx/ --summarize --human-readable --recursive | awk '{print $5}' | egrep '\.vcf$' | sed 's/.vcf$//' | sort) | sed 's/^/s3:\/\/quantgene-portland-pgx\//; s/$/.vcf/' | ./get_pgx_result.sh