Merge pull request #84 from nesi/dini-dev

fixing bugs related to snakemake profile and correct the order in submit.sh

08-snakemake/profiles/slurm/CookieCutter.py

@@ -0,0 +1,39 @@
+#
+# Based on lsf CookieCutter.py
+#
+import os
+import json
+
+d = os.path.dirname(__file__)
+with open(os.path.join(d, "settings.json")) as fh:
+    settings = json.load(fh)
+
+
+def from_entry_or_env(values, key):
+    """Return value from ``values`` and override with environment variables."""
+    if key in os.environ:
+        return os.environ[key]
+    else:
+        return values[key]
+
+
+class CookieCutter:
+
+    SBATCH_DEFAULTS = from_entry_or_env(settings, "SBATCH_DEFAULTS")
+    CLUSTER_NAME = from_entry_or_env(settings, "CLUSTER_NAME")
+    CLUSTER_CONFIG = from_entry_or_env(settings, "CLUSTER_CONFIG")
+
+    @staticmethod
+    def get_cluster_option() -> str:
+        cluster = CookieCutter.CLUSTER_NAME
+        if cluster != "":
+            return f"--cluster={cluster}"
+        return ""
+
+    @staticmethod
+    def get_cluster_logpath() -> str:
+        return "logs/slurm/%r/%j"
+
+    @staticmethod
+    def get_cluster_jobname() -> str:
+        return "%r_%w"

08-snakemake/profiles/slurm/config.yaml

@@ -0,0 +1,29 @@
+
+cluster-sidecar: "slurm-sidecar.py"
+cluster-cancel: "scancel"
+restart-times: "2"
+jobscript: "slurm-jobscript.sh"
+cluster: "slurm-submit.py"
+cluster-status: "slurm-status.py"
+max-jobs-per-second: "10"
+max-status-checks-per-second: "10"
+local-cores: 1
+latency-wait: "5"
+use-conda: "False"
+use-singularity: "False"
+jobs: "500"
+printshellcmds: "True"
+
+# Example resource configuration
+# default-resources:
+#   - runtime=100
+#   - mem_mb=6000
+#   - disk_mb=1000000
+# # set-threads: map rule names to threads
+# set-threads:
+#   - single_core_rule=1
+#   - multi_core_rule=10
+# # set-resources: map rule names to resources in general
+# set-resources:
+#   - high_memory_rule:mem_mb=12000
+#   - long_running_rule:runtime=1200

08-snakemake/profiles/slurm/settings.json

@@ -0,0 +1,5 @@
+{
+    "SBATCH_DEFAULTS": "",
+    "CLUSTER_NAME": "eri",
+    "CLUSTER_CONFIG": ""
+}

08-snakemake/profiles/slurm/slurm-jobscript.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+# properties = {properties}
+{exec_job}