GMS Commands

Import sample data. (Needs to have own dir for BAMS/CRAMS?)

for file in $(ls *R1.fastq.gz); do 
	sample=$(echo $file | cut -d'R' -f1| rev | cut -c2- | rev)
	genome sample create --name=${sample} --common-name "tumor" --tissue-desc "blood" --extraction-type "dna"
	genome library create --sample ${sample} --name ${sample}_lib1
	genome instrument-data import trusted-data --analysis-project=2f3b33df3bee447089fd722946de7777 --import-source-name BMT --library ${sample}_lib1 --source-directory /storage1/fs1/bolton/Active/projects/BMT/BMT_data/${sample} --import-format fastq --description "${sample} Haloplex BMT" --read-count 1;
done