Added scripts for archiving trio whole exomes, archive path in config file

submit_trio_wes_archive_project.sh

+#!/bin/bash
+#PBS -l walltime=24:00:00
+#PBS -l ncpus=1,mem=2gb
+#PBS -q uv2000
+#PBS -N trio_whole_exome_archive_project
+#PBS -j oe
+
+# Expects environment variables to be set
+# PROJECT_ID - e.g. 12345_LastnameFirstname
+# PRIORITY_DIRS - e.g. 05122019,07122019 (colon delimited if more than one)
+# CONFIG_SH - absolute path to configuration script setting environment variables
+
+# Source the configuration file
+source $CONFIG_SH
+
+# Move to the output directory
+cd $OUTPUT_DIR
+
+# Copy bcbio output files
+rsync -av *_$PROJECT_DIR* $ARCHIVE_DIR/
+
+# Copy qc files
+cd qc
+mkdir -p $ARCHIVE_DIR/qc
+rsync -av $PROJECT_DIR* $ARCHIVE_DIR/qc/
+
+# Copy prioritization files
+cd ../prioritization
+mkdir -p $ARCHIVE_DIR/prioritization
+
+DIRS=$(echo $PRIORITY_DIRS | tr ":" "\n")
+
+for dir in $DIRS
+do
+  rsync -av $DIR $ARCHIVE_DIR/prioritization/
+done
+
+# move to the archive area and check the md5s
+cd $ARCHIVE_DIR
+
+for family_dir in *_$PROJECT_DIR*
+do
+  cd $family_dir
+  md5sum --check md5sum.txt
+  cd ..
+done
+
+cd qc
+md5sum --check ${PROJECT_ID}_qc_report.md5sum.txt
+
+cd ../prioritization
+
+for dir in $DIRS
+do
+  cd $dir
+  md5sum --check ../$dir.md5sum.txt
+  cd ..
+done
+

submit_trio_wes_priority_and_qc_checksums.sh

+#!/bin/bash
+#PBS -l walltime=48:00:00
+#PBS -l ncpus=1,mem=2gb
+#PBS -q sgp
+#PBS -N trio_whole_exome_priority_and_qc_checksums
+#PBS -j oe
+
+# Expects environment variables to be set
+# PROJECT_ID - e.g. 12345_LastnameFirstname
+# PRIORITY_DIRS - e.g. 05122019,07122019 (colon delimited if more than one)
+# CONFIG_SH - absolute path to configuration script setting environment variables
+
+source $CONFIG_SH
+
+# calculate checksums on the qc files for this project
+
+cd $OUTPUT_DIR/qc
+
+md5sum ${PROJECT_ID}_qc_report.html > ${PROJECT_ID}_qc_report.md5sum.txt
+
+for file in `find ${PROJECT_ID}_qc_report_data -type f`
+do
+  md5sum $file >> ${PROJECT_ID}_qc_report.md5sum.txt
+done
+
+# calculate checksusms on the prioritization files for this project
+
+cd $OUTPUT_DIR/prioritization
+
+DIRS=$(echo $PRIORITY_DIRS | tr ":" "\n")
+
+for dir in $DIRS
+do
+  cd $dir
+
+  rm ../$dir.md5sum.txt 2> /dev/null
+
+  for file in `find . -type f`
+  do
+    md5sum $file >> ../$dir.md5sum.txt
+  done
+
+  cd ..
+done
+
+

trio_whole_exome_config.sh

@@ -16,4 +16,6 @@ CONFIG_DIR=$BASE/config
 WORK_DIR=$BASE/work
 OUTPUT_DIR=$BASE/output
 
+ARCHIVE_DIR=/archive/u027/trio_whole_exome
+
 export PATH=/home/u027/project/software/bcbio/tools/bin:$PATH