submitGadi.pbs

#!/bin/bash
#PBS -P xe2
#PBS -q normal
#PBS -l walltime=10:00:00
#PBS -l mem=4G
#PBS -l jobfs=100GB
#PBS -l ncpus=1
#PBS -l storage=scratch/xe2+gdata/xe2
#PBS -l wd

eval "$(/g/data/xe2/gadi/conda/bin/conda shell.zsh hook)" ##useconda
conda activate sf-snake
set -euo pipefail # safe mode
set -x # logging

TARGET=${TARGET:-all}

QSUB="qsub -q {cluster.queue} -l ncpus={threads} -l jobfs={cluster.hdd}"
QSUB="$QSUB -l walltime={cluster.time} -l mem={cluster.mem} -N {rule} -l storage={cluster.storage}"
QSUB="$QSUB -l wd -j oe -P {cluster.project}"

snakemake										\
	--use-conda                               	\
    -j 1000                                   	\
    --max-jobs-per-second 2                   	\
    --cluster-config cluster-configs/pbs.yaml 	\
    --local-cores ${PBS_NCPUS:-1}             	\
    --js profiles/pbs/jobscript.sh            	\
    --nolock                                  	\
    --rerun-incomplete                        	\
    --keep-going                              	\
    --cluster "$QSUB"                         	\
    "$TARGET"


# Before running this, initialise conda environments by running this is a copyq (internet access) job:
# snakemake -j 1 --conda-create-envs-only --use-conda