5.2 Populate the tracking database with the S3 paths for the samples to be processed

After inputting the sample information, users need to input the location of the sequencing file to process into the tracking database. This can be done using the following command:

function rawurlencode(){
echo -n "$1" | perl -pe 's/([^a-zA-Z0-9_.!~*()'\''-])/sprintf("%%%02X", ord($1))/ge' | perl -pe 's/(\W)/sprintf("%%%02X", ord($1))/ge'
}

s3='s3://YOUR/DATA/PATH.bam'    ### S3 path for each of the samples to be processed 
seqfile_s3_path=$(rawurlencode $s3)

curl -sS "http://IP/v1/sample/set-attr/seqfile_s3_uri/${project_id}/${sample_name}/${seqfile_s3_path}"

where

a) project_id: this is the project ID outputted by Section 3.2

b) sample_name: sample name (note this needs to match the sample name of the input file in the S3 bucket)

c) s3_path: S3 path of the input sequencing file