Updated paths to u035

submit_bcbio_trio_wes.sh

 #!/bin/bash
 #PBS -l walltime=48:00:00
 #PBS -l ncpus=16,mem=8gb
-#PBS -q sgp
+#PBS -q uv2000
 #PBS -N trio_whole_exome_bcbio
 #PBS -j oe
 
@@ -22,6 +22,12 @@ fi
 
 source $CONFIG_SH
 
+echo $SCRIPTS
+echo $BCBIO_TEMPLATE
+echo $BASE
+
+exit
+
 FAMILY_ID=`head -n $PBS_ARRAY_INDEX $PARAMS_DIR/$PROJECT_ID.family_ids.txt | tail -n 1`
 
 CONFIG_FILE=$CONFIG_DIR/${PROJECT_ID}_${FAMILY_ID}.yaml

submit_trio_wes_aspera_download.sh

@@ -7,18 +7,18 @@
 
 source $TRANSFER_INFO_FILE
 
-TIMELOG=/home/u027/project/trio_whole_exome/logs/project/$PROJECT.log
+TIMELOG=/home/u035/project/trio_whole_exome/logs/project/$PROJECT.log
 
 echo $PROJECT submit_trio_wes_aspera_download.sh start `date` >> $TIMELOG
 
 
-/home/u027/project/software/aspera/connect/bin/ascp \
+/home/u035/project/software/aspera/connect/bin/ascp \
   -T -P 33001 -O 33001 -l 500M -k2 --overwrite=diff \
   $ASPERA_SCP_USER@transfer.genomics.ed.ac.uk:$PROJECT \
-  /scratch/u027/project/trio_whole_exome/data
+  /scratch/u035/project/trio_whole_exome/data
 
 
-cd /scratch/u027/project/trio_whole_exome/data/$PROJECT/raw_data
+cd /scratch/u035/project/trio_whole_exome/data/$PROJECT/raw_data
 
 
 rm ../md5_check.txt 2> /dev/null

trio_whole_exome_bcbio_template.yaml

@@ -16,4 +16,4 @@ details:
   analysis: variant2
   genome_build: hg38
 upload:
-  dir: /scratch/u027/project/trio_whole_exome/analysis/output
+  dir: /scratch/u035/project/trio_whole_exome/analysis/output

trio_whole_exome_config.sh

@@ -3,19 +3,19 @@
 # Basic configuration options for trio WES pipeline
 #
 
-SCRIPTS=/home/u027/project/scripts
+SCRIPTS=/home/u035/project/scripts
 BCBIO_TEMPLATE=$SCRIPTS/trio_whole_exome_bcbio_template.yaml
-TARGET=/home/u027/project/resources/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
-DOWNLOAD_DIR=/scratch/u027/project/trio_whole_exome/data
-REFERENCE_GENOME=/home/u027/project/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
+TARGET=/home/u035/project/resources/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
+DOWNLOAD_DIR=/scratch/u035/project/trio_whole_exome/data
+REFERENCE_GENOME=/home/u035/project/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
 
-BASE=/scratch/u027/project/trio_whole_exome/analysis
+BASE=/scratch/u035/project/trio_whole_exome/analysis
 PARAMS_DIR=$BASE/params
 READS_DIR=$BASE/reads
 CONFIG_DIR=$BASE/config
 WORK_DIR=$BASE/work
 OUTPUT_DIR=$BASE/output
 
-ARCHIVE_DIR=/archive/u027/trio_whole_exome
+ARCHIVE_DIR=/archive/u035/trio_whole_exome
 
-export PATH=/home/u027/project/software/bcbio/tools/bin:$PATH
+export PATH=/home/u035/project/software/bcbio/bin:$PATH