bpcp

Script to batch process images using CellProfiler and GNU parallel

Notes

• Requirements
• sudo apt-get install parallel -y
• sudo apt-get install python-pip -y
• pip install awscli
• aws configure
• Before launching, figure out memory requirements of your pipeline (optional)
• valgrind --tool=massif --depth=1 --trace-children=yes <cmd>
• To create RAM disk
• mkdir /mnt/ramdisk
• sudo mount -t tmpfs -o size=24576m tmpfs /mnt/ramdisk
• On the command line use -t /mnt/ramdisk
• sample usage ./run_analysis_pipeline.sh -d <DATASET> -p <PIPELINE> -t /mnt/ramdisk