From cdb153d4e2c92cc84d4999271e80e4681ab43c5e Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Wed, 19 Aug 2020 10:38:37 +0100
Subject: [PATCH] Updated paths to u035
---
submit_bcbio_trio_wes.sh | 8 +++++++-
submit_trio_wes_aspera_download.sh | 8 ++++----
trio_whole_exome_bcbio_template.yaml | 2 +-
trio_whole_exome_config.sh | 14 +++++++-------
4 files changed, 19 insertions(+), 13 deletions(-)
diff --git a/submit_bcbio_trio_wes.sh b/submit_bcbio_trio_wes.sh
index a03a424..adefd18 100755
--- a/submit_bcbio_trio_wes.sh
+++ b/submit_bcbio_trio_wes.sh
@@ -1,7 +1,7 @@
#!/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
diff --git a/submit_trio_wes_aspera_download.sh b/submit_trio_wes_aspera_download.sh
index 5a6d0fa..8bad263 100755
--- a/submit_trio_wes_aspera_download.sh
+++ b/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
diff --git a/trio_whole_exome_bcbio_template.yaml b/trio_whole_exome_bcbio_template.yaml
index c4a3102..e960be9 100644
--- a/trio_whole_exome_bcbio_template.yaml
+++ b/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
diff --git a/trio_whole_exome_config.sh b/trio_whole_exome_config.sh
index 7c0e714..4b46a78 100644
--- a/trio_whole_exome_config.sh
+++ b/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
--
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