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Examples_submit_on_cluster.md

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Examples of how to run the sumstat enrichment test on a cluster

Before using these commands, find out what job submission system is installed on your organization's cluster and what are the guidelines for using your cluster. Here we list examples when using a SUN Grid Engine (SGE).

Run these commands from the root of your project folder (polysel). Set projectname according to one of the examples (primates_homininae, humanpops, altitude). You can add your own project name and set its parameters in the files polysel_shufflesets_cluster.sh and polysel_cluster.sh.

###SUN Grid Engine job submission system###

STEP 1: run polysel_shufflesets_cluster.sh script with:

Change to for i in {1..3} if you just want to try out if everything is working correctly.
Change to for i in {1..200} to reproduce the humanpops and altitude results

  # make script executable (only need to run once)
  chmod +x ./script/polysel_shufflesets_cluster.sh

  projectname="primates_homininae"

  for i in {1..300}
  do
  qsub -l h_cpu=10:00:00 -l h_vmem=4G -o ./log/shuffle${i}_${projectname}.out \
  -e ./log/shuffle${i}_${projectname}.err -cwd -N shuffle${i}_${projectname} \
  ./script/polysel_shufflesets_cluster.sh $i $projectname
  done

or (USING SCRATCH): run polysel_shufflesets_cluster_scratch.sh script with:

  # make script executable (only need to run once)
  chmod +x ./script/polysel_shufflesets_cluster_scratch.sh

  projectname="primates_homininae"

  for i in {1..300}
  do
  qsub -l h_cpu=10:00:00 -l h_vmem=4G -o ./log/shuffle${i}_${projectname}.out \
  -e ./log/shuffle${i}_${projectname}.err -cwd -N shuffle${i}_${projectname} \
  ./script/polysel_shufflesets_cluster_scratch.sh $i $projectname
  done

STEP 2: run polysel_cluster.sh script with:

  # make script executable (only need to run once)
  chmod +x ./script/polysel_cluster.sh

  projectname="primates_homininae"
  
  qsub -l h_cpu=10:00:00 -l h_vmem=4G -o ./log/${projectname}.out \
  -e ./log/${projectname}.err -cwd -N ${projectname} \
  ./script/polysel_cluster.sh $projectname

or: (USING SCRATCH): run polysel_cluster_scratch script with:

  # make script executable (only need to run once)
  chmod +x ./script/polysel_cluster_scratch.sh

  projectname="primates_homininae"

  qsub -l h_cpu=10:00:00 -l h_vmem=4G -o ./log/${projectname}.out \
  -e ./log/${projectname}.err -cwd -N ${projectname} \
  ./script/polysel_cluster_scratch.sh $projectname