From 894a5f84f3eedef23e99cc226c38123d48b62ed2 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 13 Aug 2020 10:45:06 -0500
Subject: [PATCH] Allow study script to run on cluster
---
README.md | 3 ++-
workflow/scripts/splitStudy.sh | 6 ++++++
2 files changed, 8 insertions(+), 1 deletion(-)
diff --git a/README.md b/README.md
index a4b6f56..2216c27 100644
--- a/README.md
+++ b/README.md
@@ -62,7 +62,8 @@ To run a set of replicates from study RID:
------------------------------------------
Run in repo root dir:
* `sh workflow/scripts/splitStudy.sh [studyRID]`
-It will run in parallel in batches of 25 replicatesRID with 30 second delays between launches.
+It will run in parallel in batches of 25 replicatesRID with 30 second delays between launches.\
+NOTE: Nextflow "local" processes for all replicates will run on the node/machine the bash script is launched from... consider running the study script on the BioHPC's SLURM cluster (use `sbatch`).
diff --git a/workflow/scripts/splitStudy.sh b/workflow/scripts/splitStudy.sh
index bade44b..0af729d 100644
--- a/workflow/scripts/splitStudy.sh
+++ b/workflow/scripts/splitStudy.sh
@@ -1,5 +1,11 @@
#!/bin/bash
+#SBATCH -p super
+#SBATCH --job-name GUDMAP-RBK_Study
+#SBATCH -t 7-0:0:0
+#SBATCH -o job_%j.out
+#SBATCH -e job_%j.out
+
# query GUDMAP/RBK for study RID
echo "curl --location --request GET 'https://www.gudmap.org/ermrest/catalog/2/entity/RNASeq:Replicate/Study_RID="${1}"'" | bash > $1_studyRID.json
--
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