From 8ff49ea0f18360b995f24d34ca1a5745255e1a5f Mon Sep 17 00:00:00 2001
From: Maciej Bak <maciej.bak@unibas.ch>
Date: Mon, 16 Aug 2021 21:02:30 +0200
Subject: [PATCH] hardcode cluster log relative path into the slurm profiles
---
profiles/slurm-conda/config.yaml | 1 +
profiles/slurm-singularity/config.yaml | 1 +
resources/config_schema.json | 4 ++++
workflow/Snakefile | 11 ++++++-----
4 files changed, 12 insertions(+), 5 deletions(-)
diff --git a/profiles/slurm-conda/config.yaml b/profiles/slurm-conda/config.yaml
index 2fb0969..dcf0976 100644
--- a/profiles/slurm-conda/config.yaml
+++ b/profiles/slurm-conda/config.yaml
@@ -1,6 +1,7 @@
jobscript: "../slurm-jobscript.sh"
cluster: "../slurm-submit.py"
cluster-status: "../slurm-status.py"
+config: "cluster_logs='logs/cluster'"
snakefile: "../../workflow/Snakefile"
cores: 256
jobs: 256
diff --git a/profiles/slurm-singularity/config.yaml b/profiles/slurm-singularity/config.yaml
index 4fc0a6b..960bee6 100644
--- a/profiles/slurm-singularity/config.yaml
+++ b/profiles/slurm-singularity/config.yaml
@@ -1,6 +1,7 @@
jobscript: "../slurm-jobscript.sh"
cluster: "../slurm-submit.py"
cluster-status: "../slurm-status.py"
+config: "cluster_logs='logs/cluster'"
snakefile: "../../workflow/Snakefile"
cores: 256
jobs: 256
diff --git a/resources/config_schema.json b/resources/config_schema.json
index 1ad7846..299c43a 100644
--- a/resources/config_schema.json
+++ b/resources/config_schema.json
@@ -17,6 +17,10 @@
"type": "string",
"description": "Path to log directory."
},
+ "cluster_logs": {
+ "type": "string",
+ "description": "Path to cluster log directory."
+ },
"kallisto_indexes": {
"type": "string",
"description": "Path to kallisto indexes directory."
diff --git a/workflow/Snakefile b/workflow/Snakefile
index d5ac1ea..210c077 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -38,11 +38,12 @@ except KeyError:
logger.warning(f"No rule config specified: using default values for all tools.")
# Create dir for cluster logs, if applicable
-if cluster_config:
- os.makedirs(
- os.path.join(
- os.getcwd(),
- os.path.dirname(cluster_config['__default__']['out']),
+onstart:
+ if config["cluster_logs"]:
+ os.makedirs(
+ os.path.join(
+ os.getcwd(),
+ config["cluster_logs"],
),
exist_ok=True)
--
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