From 55e0eef24116c832b2a3afa9e5da59ece68132d0 Mon Sep 17 00:00:00 2001
From: not populated not populated <ameynert@sdf-cs1.eidf.epcc.ed.ac.uk>
Date: Thu, 30 Sep 2021 13:51:26 +0100
Subject: [PATCH] First attempt at sbatch command for slurm system
---
...SOP_alignment_variant_annotation_ultra2.md | 4 +--
submit_bcbio_trio_wes.sh | 32 +++++++++++--------
2 files changed, 20 insertions(+), 16 deletions(-)
diff --git a/docs/SOP_alignment_variant_annotation_ultra2.md b/docs/SOP_alignment_variant_annotation_ultra2.md
index 63157a0..4d09433 100644
--- a/docs/SOP_alignment_variant_annotation_ultra2.md
+++ b/docs/SOP_alignment_variant_annotation_ultra2.md
@@ -161,8 +161,8 @@ X=`wc -l $PARAMS_DIR/$project_id.family_ids.txt | awk '{print $1}'`
```
cd /home/u035/u035/shared/trio_whole_exome/analysis/logs
-qsub -v PROJECT_ID=$project_id,VERSION=$version,CONFIG_SH=/home/u035/u035/shared/scripts/trio_whole_exome_config.sh \
- -J 1-$X -N trio_whole_exome_bcbio.$project_id \
+sbatch --export=PROJECT_ID=$project_id,VERSION=$version,CONFIG_SH=/home/u035/u035/shared/scripts/trio_whole_exome_config.sh \
+ --array=1-$X --job-name=trio_whole_exome_bcbio.$project_id \
/home/u035/u035/shared/scripts/submit_bcbio_trio_wes.sh
```
diff --git a/submit_bcbio_trio_wes.sh b/submit_bcbio_trio_wes.sh
index d07d9eb..9b096b3 100755
--- a/submit_bcbio_trio_wes.sh
+++ b/submit_bcbio_trio_wes.sh
@@ -1,18 +1,19 @@
#!/bin/bash
-#PBS -l walltime=48:00:00
-#PBS -l ncpus=16,mem=8gb
-#PBS -q sgp
-#PBS -N trio_whole_exome_bcbio
-#PBS -j oe
+#SBATCH --cpus-per-task 16
+#SBATCH --mem=8GB
+#SBATCH --time=48:00:00
+#SBATCH --job-name=trio_whole_exome_bcbio
+#SBATCH --output=trio_whole_exome_bcbio.%A_%a.out
+#SBATCH --error=trio_whole_exome_bcbio.%A_%a.err
# enable running singletons
-if [ -z $PBS_ARRAY_INDEX ]
+if [ -z $SLURM_ARRAY_TASK_ID ]
then
if [ -z $INDEX ]
then
- export PBS_ARRAY_INDEX=1
+ export SLURM_ARRAY_TASK_ID=1
else
- export PBS_ARRAY_INDEX=$INDEX
+ export SLURM_ARRAY_TASK_ID=$INDEX
fi
fi
@@ -23,19 +24,23 @@ fi
source $CONFIG_SH
-FAMILY_ID=`head -n $PBS_ARRAY_INDEX $PARAMS_DIR/$PROJECT_ID.family_ids.txt | tail -n 1`
+FAMILY_ID=`head -n $SLURM_ARRAY_TASK_ID $PARAMS_DIR/$PROJECT_ID.family_ids.txt | tail -n 1`
-CONFIG_FILE=$CONFIG_DIR/${VERSION}_${PROJECT_ID}_${FAMILY_ID}.yaml
+SHORT_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'`
+
+CONFIG_FILE=$CONFIG_DIR/${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID}.yaml
mkdir -p $WORK_DIR/$FAMILY_ID
cd $WORK_DIR/$FAMILY_ID
-bcbio_nextgen.py $CONFIG_FILE -n 16 -t local
+bcbio_nextgen.py $CONFIG_FILE -n $SLURM_CPUS_PER_TASK -t local
+
+exit
DATE=$(basename `tail log/bcbio-nextgen.log | grep 'Storing in local filesystem' | tail -n 1 | awk '{ print $6 }' | perl -pe "s/_${PROJECT_ID}.+//"`)
-if [ -e $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID} ]
+if [ -e $OUTPUT_DIR/${DATE}_${SHORT_PROJECT_ID}_${FAMILY_ID} ]
then
- for INDV in `cut -f 2 $PARAMS_DIR/${PROJECT_ID}_${FAMILY_ID}.ped`
+ for INDV in `cut -f 2 $OUTPUT_DIR/${SHORT_PROJECT_ID}_${VERSION}/params/${PROJECT_ID}_${FAMILY_ID}.ped`
do
mv $OUTPUT_DIR/$INDV $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID}/
done
@@ -53,4 +58,3 @@ then
else
echo $OUTPUT_DIR/${DATE}_${PROJECT_ID}_${FAMILY_ID} does not exist.
fi
-
--
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