add scripts necessary for shark

ATAC-seq_pipeline/slurm-cluster-status.py

+#!/usr/bin/env python3
+import argparse
+import subprocess
+import time
+
+STATE_MAP = {
+    "BOOT_FAIL": "failed",
+    "CANCELLED": "failed",
+    "COMPLETED": "success",
+    "CONFIGURING": "running",
+    "COMPLETING": "running",
+    "DEADLINE": "failed",
+    "FAILED": "failed",
+    "NODE_FAIL": "failed",
+    "OUT_OF_MEMORY": "failed",
+    "PENDING": "running",
+    "PREEMPTED": "failed",
+    "RUNNING": "running",
+    "RESIZING": "running",
+    "SUSPENDED": "running",
+    "TIMEOUT": "failed"
+}
+
+
+def fetch_status(batch_id, attempts: int = 3, wait_time_seconds: float = 3):
+    """fetch the status for the batch id"""
+    sacct_args = ["sacct", "-j",  batch_id, "-o", "State", "--parsable2",
+                  "--noheader"]
+
+    for _ in range(attempts):
+        output = subprocess.check_output(sacct_args).decode("utf-8").strip()
+        if output:
+            break
+        time.sleep(wait_time_seconds)
+    else:
+        raise TimeoutError(f"Failed to get state for job id: {batch_id}.")
+
+    # The first output is the state of the overall job
+    # See
+    # https://stackoverflow.com/questions/52447602/slurm-sacct-shows-batch-and-extern-job-names
+    # for details
+    job_status = output.split("\n")[0]
+
+    # If the job was cancelled manually, it will say by who, e.g "CANCELLED by 12345"
+    # We only care that it was cancelled
+    if job_status.startswith("CANCELLED by"):
+        return "CANCELLED"
+
+    # Otherwise, return the status
+    try:
+        return STATE_MAP[job_status]
+    except KeyError:
+        raise NotImplementedError(f"Encountered unknown status {job_status} "
+                                  f"when parsing output:\n{output}")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("batch_id", type=str)
+    args = parser.parse_args()
+
+    status = fetch_status(args.batch_id)
+    print(status)

ATAC-seq_pipeline/slurm_minisnakemake.sh

+#! /bin/bash
+
+#SBATCH  --job-name=mini_snakemake
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user j.chouaref@lumc.nl
+#SBATCH -t 48:00:00
+#SBATCH --mem=60000
+
+
+echo Start time : `date`
+snakemake -p \
+        --snakefile Snakefile \
+        --latency-wait 60 \
+        --wait-for-files \
+        --rerun-incomplete \
+        --use-conda \
+        --cluster "sbatch --parsable --partition=all --mem=60g --ntasks=1 --cpus-per-task=8 --time=60:00:00 --hint=multithread" \
+        --cluster-status "./slurm-cluster-status.py" \
+       	--jobs 30
+
+
+echo End time : `date`
+