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