First draft of Slurm params

submit_trio_wes_checksums.sh

 #!/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
-