From cc66bb22ac057b9e1324fb77def903608ac22d8f Mon Sep 17 00:00:00 2001
From: not populated not populated <ameynert@sdf-cs1.eidf.epcc.ed.ac.uk>
Date: Mon, 4 Oct 2021 13:22:18 +0100
Subject: [PATCH] First draft of Slurm params
---
submit_trio_wes_checksums.sh | 33 +++++++++++----------------------
1 file changed, 11 insertions(+), 22 deletions(-)
diff --git a/submit_trio_wes_checksums.sh b/submit_trio_wes_checksums.sh
index b67cba4..ca6bbba 100755
--- a/submit_trio_wes_checksums.sh
+++ b/submit_trio_wes_checksums.sh
@@ -1,20 +1,10 @@
#!/bin/bash
-#PBS -l walltime=48:00:00
-#PBS -l ncpus=1,mem=2gb
-#PBS -q uv2000
-#PBS -N trio_whole_exome_checksums
-#PBS -j oe
-
-# enable running singletons
-if [ -z $PBS_ARRAY_INDEX ]
-then
- if [ -z $INDEX ]
- then
- export PBS_ARRAY_INDX=1
- else
- export PBS_ARRAY_INDEX=$INDEX
- fi
-fi
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=2GB
+#SBATCH --time=6:00:00
+#SBATCH --job-name=trio_whole_exome_checksums
+#SBATCH --output=trio_whole_exome_checksums.%A_%a.out
+#SBATCH --error=trio_whole_exome_checksums.%A_%a.err
# Expects environment variables to be set
# PROJECT_ID - e.g. 12345_LastnameFirstname
@@ -23,13 +13,13 @@ 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`
-BASE_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'`
+SHORT_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'`
-# This assumes that ${VERSION}_${PROJECT_ID}_${FAMILY_ID} is unique, and it should be - if there was
-# a re-run of a family, it should have a new project id.
-cd $OUTPUT_DIR/${VERSION}_${BASE_PROJECT_ID}/*${VERSION}_${PROJECT_ID}_${FAMILY_ID}*
+# This assumes that ${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID} is unique, and it should be -
+# if there was a re-run of a family, it should have a new project id and version.
+cd $OUTPUT_DIR/${SHORT_PROJECT_ID}_${VERSION}/families/*${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID}
rm md5sum.txt 2> /dev/null
@@ -37,4 +27,3 @@ for file in `find . -type f | grep -v '\.bam'`
do
md5sum $file >> md5sum.txt
done
-
--
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