Add apptainer support

apptainer.py

@@ -0,0 +1,66 @@
+import argparse
+import json
+import os
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument('-c', type=str, help='Path to config file')
+parser.add_argument('-t', type=str, help='Thread count')
+parser.add_argument('-o', type=str, help='Output directory')
+parser.add_argument('-m', type=int, default=10, help='Memory limit in GB, default: 10')
+parser.add_argument('-i', type=str,
+                    help='[Optional] Docker image, only for development purposes')
+parser.add_argument('-s', type=str, default=None, help='Slurm partition')
+
+args = parser.parse_args()
+
+
+def process_configs(configs: dict) -> dict:
+    mounts = {}
+    for key, value in configs.items():
+        if isinstance(value, dict):
+            mounts.update(process_configs(value))
+        else:
+            if isinstance(value, str) and os.path.exists(value):
+                extension = os.path.splitext(value)[1]
+                inside_path = f"/srv/input/{key}{extension}"
+                mounts[inside_path] = os.path.abspath(value)
+
+                configs[key] = inside_path
+    return mounts
+
+
+image = args.i if args.i else "nicotru/tf-prioritizer:master"
+config_path = os.path.abspath(args.c)
+threads = args.t
+output = os.path.abspath(args.o)
+memory = args.m
+slurm_partition = args.s
+
+os.makedirs(output, exist_ok=True)
+
+with open(config_path, 'r') as f:
+    configs = json.load(f)
+
+mounts = process_configs(configs)
+
+docker_config_file = os.path.join(os.path.dirname(output), 'docker_config.json')
+
+with open(docker_config_file, 'w') as f:
+    json.dump(configs, f, indent=4)
+
+volume_string = ' '.join([f'-B {v}:{k}:ro' for k, v in mounts.items()])
+
+internal_command = f"java -Xmx{memory}g -jar /srv/TF-Prioritizer.jar -t {threads} -o /srv/wd -c /srv/input/configs.json"
+
+external_command = f"apptainer run " \
+                   f" -B {docker_config_file}:/srv/input/configs.json:ro {volume_string} -B {output}:/srv/wd:rw " \
+                   f"docker://{image} {internal_command}"
+
+slurm_prefix = f"srun -p {slurm_partition} --cpus-per-task={threads} --mem={memory}G --output={output}/slurm-%j.out " \
+               f"--error={output}/slurm-%j.err" if slurm_partition else ""
+
+if not args.i:
+    os.system("docker image pull " + image)
+
+os.system(slurm_prefix + external_command)