Ruche Testing

Author: HakimBenkirane

config/benchmark_union_cpu.yml config/benchmark_union_local.yml

@@ -1,6 +1,6 @@
 dataset:
-  data_dir: '../../data/spatial'
-  metadata-file: 'metadata_2024_06_21.csv'
+  data_dir: './../data/spatial/'
+  metadata_file: 'metadata_2024_06_21.csv'
   tissues: ['ovarian']
   mode: 'union'
 

config/benchmark_union_ruche.yml

@@ -0,0 +1,17 @@
+dataset:
+  data_dir: '/gpfs/workdir/shared/prime/spatial/all/'
+  metadata_file: 'metadata_2024_06_21.csv'
+  tissues: ['breast']
+  mode: 'union'
+
+params:
+  model_names: ['STAGATE', 'SEDR', 'SpaceFlow', 'GraphST']
+  hidden_dim: 64
+  batch_key: 'slide_id'
+  device: 'cuda'
+  fast_dev_run: True
+  n_clusters: 7
+
+  
+
+

main.py

@@ -27,7 +27,7 @@ def load_yaml(file_path):
     for tissue in config['dataset']['tissues']:
         print('----- ', tissue, '\n')
 
-        dataset = AnnDataset(data_dir='../../data/spatial', metadata_filename='metadata_2024_06_21.csv')
+        dataset = AnnDataset(data_dir=config['dataset']['data_dir'], metadata_filename=config['dataset']['metadata_file'])
         adataset = dataset.load_data(tissue_types=[tissue], mode=config['dataset']['mode'])
 
         print("------------ Dataset Loaded ! ----------------\n")

remote/slurm_main_cpu.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+#SBATCH --job-name=Novae_benchmark
+#SBATCH --output=%x_%j.out
+#SBATCH --ntasks=1
+#SBATCH [email protected]
+#SBATCH --cpus-per-task=4
+#SBATCH --gres=gpu:2
+#SBATCH --partition=gpu
+#SBATCH --mem=256000
+#SBATCH --exclude=ruche-gpu01
+
+# Modules load
+module load anaconda3/2021.05/gcc-9.2.0
+module load cuda/12.2.1/gcc-11.2.0 
+
+source activate novae_benchmark
+
+python -u main.py -c config/benchmark_union_ruche.yml
+
+
+
+
+