Updated download from EdGe

old_submit_trio_wes_aspera_download.sh

+#!/bin/bash
+#PBS -l walltime=24:00:00
+#PBS -l ncpus=1,mem=4gb
+#PBS -q uv2000
+#PBS -N aspera
+#PBS -j oe
+
+source $TRANSFER_INFO_FILE
+
+/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/u035/project/trio_whole_exome/data
+
+cd /scratch/u035/project/trio_whole_exome/data/$PROJECT/raw_data
+
+rm ../md5_check.txt 2> /dev/null
+for DATE in 20*[0-9]
+do
+  cd $DATE
+  md5sum --check md5sums.txt >> ../../md5_check.txt
+  cd ..
+done

submit_trio_wes_lftp_download.sh

+#!/bin/bash
+#PBS -l walltime=24:00:00
+#PBS -l ncpus=1,mem=4gb
+#PBS -q uv2000
+#PBS -N lftp
+#PBS -j oe
+
+###source $TRANSFER_INFO_FILE
+###/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/raw_data \
+###  /scratch/u035/project/trio_whole_exome/data
+
+
+PROJ_CONN="login anonymous lftp@ ; mirror -vv ${TOKEN}/${PROJECT}/raw_data  ."
+echo ${PROJ_CONN}
+
+
+# set up an EPCC folder for this project
+mkdir /scratch/u035/project/trio_whole_exome/data/$PROJECT
+cd /scratch/u035/project/trio_whole_exome/data/$PROJECT
+
+
+# download the data
+lftp transfer.genomics.ed.ac.uk <<<${PROJ_CONN}
+
+
+# go into raw_data to perform the md5_check
+# cd /scratch/u035/project/trio_whole_exome/data/$PROJECT/raw_data
+
+rm md5_check.txt 2> /dev/null
+for DATE in 20*[0-9]
+do
+  cd $DATE
+  md5sum --check md5sums.txt >> ../md5_check.txt
+  cd ..
+done