Bacterial genome browser scripts
Most of these heavily depend on specifics of the cluster / servers I'm using at GIS.
GERMS browser Version 2 SLC 171228
Main purpose is to eliminate any manual intervention with running assembly and SNP calling on sequencing data.
General workflow:
- Prepping FASTQ files -- Download from GIS or Genbank SRA -- Collect some info and run Kraken
- Running WGS and SNP calling -- Based on Kraken result, select a reference genome -- Run WGS, SNP caling, SRST2 and put the files in the right place -- Do a database import of everything
- Cleaning up -- Check for completion -- Delete the FASTQ files
All meant to be stowed in /mnt/software/stow/GERMS_BROWSER Subdirectories and files: bin browser-staging.sh browser-species.sh lib browser-fastq.snakefile browser-snpcall.snakefile browser-database.schema etc browser-conf.sh browser-snakemake.json
Generally should be run as:
for i in ; do
while [ df $GERMS_DATA | grep -v '^Filesystem' | awk '{print $3}' -lt 50000000 ]; do
# this checks we have more than 50G available
sleep 600
done
/mnt/software/stow/GERMS_BROWSER/bin/browser-staging.sh $i && date
sleep 60
done