From 630a83751de32e25a5487931bdcae24f0951a303 Mon Sep 17 00:00:00 2001
From: bio-boris <bio-boris@users.noreply.github.com>
Date: Tue, 9 Sep 2025 10:23:41 -0500
Subject: [PATCH 1/3] Update slurm_submit to capture job ID

Modify sbatch command to output job ID
---
 scripts/slurm_submit | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/scripts/slurm_submit b/scripts/slurm_submit
index 58459d8..c3703c3 100755
--- a/scripts/slurm_submit
+++ b/scripts/slurm_submit
@@ -4,8 +4,11 @@
 # Args are submit script, outputfile, and error file
 # Return the job id via stdout
 
+module purge
+PATH=/usr/common/software/bin:/usr/common/mss/bin:/usr/common/nsg/bin:/opt/ovis/bin:/opt/ovis/sbin:/usr/local/bin:/usr/bin:/bin:/usr/lib/mit/bin:/usr/lib/mit/sbin
+
 SUBMIT=$1
 LOGFILE=$2
 ERRFILE=$3
 
-sbatch -o $LOGFILE -e $ERRFILE $SUBMIT
+sbatch -o $LOGFILE -e $ERRFILE $SUBMIT|sed 's/Submitted batch job //'

From fe50b25352d61e05a3ea82a7818078ef5c82d71d Mon Sep 17 00:00:00 2001
From: bio-boris <bio-boris@users.noreply.github.com>
Date: Tue, 9 Sep 2025 10:25:01 -0500
Subject: [PATCH 2/3] Update slurm_submit with PATH check comment

---
 scripts/slurm_submit | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/slurm_submit b/scripts/slurm_submit
index c3703c3..0f5293e 100755
--- a/scripts/slurm_submit
+++ b/scripts/slurm_submit
@@ -3,6 +3,7 @@
 # Wrapper script for Slurm batch submit
 # Args are submit script, outputfile, and error file
 # Return the job id via stdout
+# Ensure that  slurm_submit and slurm_checkjob are in the PATH . ~/.local_settings may need to be updated 
 
 module purge
 PATH=/usr/common/software/bin:/usr/common/mss/bin:/usr/common/nsg/bin:/opt/ovis/bin:/opt/ovis/sbin:/usr/local/bin:/usr/bin:/bin:/usr/lib/mit/bin:/usr/lib/mit/sbin

From f12bcd30d6359a5e4bc2fd5aa0b006f533952416 Mon Sep 17 00:00:00 2001
From: bio-boris <bio-boris@users.noreply.github.com>
Date: Tue, 9 Sep 2025 10:25:25 -0500
Subject: [PATCH 3/3] Update slurm_checkjob with PATH instructions

---
 scripts/slurm_checkjob | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/slurm_checkjob b/scripts/slurm_checkjob
index 559f26d..d919b3e 100755
--- a/scripts/slurm_checkjob
+++ b/scripts/slurm_checkjob
@@ -2,7 +2,7 @@
 # Wraper script for slurm job check
 # Args are the Job ID
 # Returns back Running, Finished, Pending or Unknown
-#
+#  Ensure that slurm_submit and slurm_checkjob are in the PATH . ~/.local_settings may need to be updated 
 JS=$(squeue -j $1 -o %t --noheader)
 
 if [ -z "$JS" ] ; then