Updated to use wget from Edinburgh Genomics

submit_trio_wes_wget_download.sh

+#!/bin/bash
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=4GB
+#SBATCH --time=24:00:00
+#SBATCH --job-name=get_data
+#SBATCH --output=get_data.%A_%a.out
+#SBATCH --error=get_data.%A_%a.err
+
+
+# setup the connection
+PROJ_CONN="ftps://transfer.genomics.ed.ac.uk/${TOKEN}/."
+echo ${PROJ_CONN}
+
+## set up an EPCC folder for this project
+#mkdir /home/u035/u035/shared/data/$PROJECT
+#cd /home/u035/u035/shared/data/$PROJECT
+cd /home/u035/u035/shared/data
+
+# download the data
+#wget -crnH --cut-dirs=1 -i - <<<'ftps://transfer.genomics.ed.ac.uk/${TOKEN}/.'
+wget -crnH --cut-dirs=1 -i - <<<${PROJ_CONN}
+
+
+
+# perform the md5_check
+cd /home/u035/u035/shared/data/$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