clean up directory structure

submitters/snakemake/Snakefile

@@ -0,0 +1,12 @@
+rule collect_and_delete:
+    input:
+        [f"{i}.txt" for i in range(100)],
+    run:
+        shell("rm {input}")
+
+
+rule create:
+    output:
+        "{i}.txt",
+    run:
+        shell("touch {output}")

submitters/snakemake/zoidberg/config.yaml

@@ -0,0 +1,9 @@
+jobscript: "grid-jobscript.sh"
+cluster: "grid-submit.py"
+cluster-status: "grid-status.py"
+max-jobs-per-second: 100
+max-status-checks-per-second: 100
+restart-times: 5
+local-cores: 10
+jobs: 5000
+verbose: false

submitters/snakemake/zoidberg/grid-jobscript.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+# properties = {properties}
+
+set -e
+
+echo "hostname:"
+hostname -f
+
+{exec_job}

submitters/snakemake/zoidberg/grid-status.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+
+import sys
+import requests
+
+resp = requests.post("http://localhost:8080/status", json=[{"id": int(sys.argv[1])}])
+
+translation = {
+    "Submitted": "running",
+    "Completed": "success",
+    "Failed": "failed",
+}
+
+print(translation[resp.json()[0]["status"]])

submitters/snakemake/zoidberg/grid-submit.py

@@ -0,0 +1,16 @@
+#!/usr/bin/env python3
+
+import sys
+import requests
+
+jobscript = sys.argv[1]
+
+resp = requests.post(
+    "http://localhost:8080/submit",
+    json=[
+        {"cmd": jobscript},
+    ],
+)
+assert resp.ok, "http request failed"
+
+print(resp.json()[0]["id"])