phenotype_reversion/parallel_eval.sh at main · pfizer-opensource/phenotype_reversion · GitHub

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#!/bin/bash
#SBATCH -o logs/2026.02.26.reproducing_results
#SBATCH -J imru
#SBATCH --time=12-00:00:00
#SBATCH --ntasks=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem=200G
#SBATCH --cpus-per-task=25
#SBATCH --nodes=1
#SBATCH --partition=defq
#--gres=gpu:1

echo " "
echo " Nodelist:= " $SLURM_JOB_NODELIST
echo " Number of nodes:= " $SLURM_JOB_NUM_NODES
echo " GPUs per node:= " $SLURM_JOB_GPUS
echo " Ntasks per node:= "  $SLURM_NTASKS_PER_NODE
echo " Run started at:- "
date

export SBATCH_EXPORT=ALL

host=$(hostname)
source ~/miniconda3/etc/profile.d/conda.sh
cd /hpfs/userws/wongd26/public/phenotype_reversion
pwd
conda activate perturb_foundation

python clear.py

python preprocessing.py --method=raw --datset=full #to process imru_full.h5ad --> raw_imru_full_processed.h5ad if you don't have it

echo "starting random analysis"
python analysis.py --method=random --dataset=full &
echo "starting scgpt analysis"
python analysis.py --method=scgpt --dataset=full &
wait
echo "starting state analysis"
python analysis.py --method=state --dataset=full &
echo "starting scimilarity analysis"
python analysis.py --method=scimilarity --dataset=full &
wait
echo "starting raw analysis"
python analysis.py --method=raw --dataset=full &
echo "starting umap analysis"
python analysis.py --method=umap --dataset=full &
wait
python misc.py
python downstream.py
echo "Run completed at:- "
date