From 16c59414dea64b1aa6a284bcf1616434c2d98eae Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Tue, 23 Mar 2021 14:56:52 +0000
Subject: [PATCH] Updated download from EdGe
---
old_submit_trio_wes_aspera_download.sh | 23 ++++++++++++++++
submit_trio_wes_lftp_download.sh | 37 ++++++++++++++++++++++++++
2 files changed, 60 insertions(+)
create mode 100755 old_submit_trio_wes_aspera_download.sh
create mode 100755 submit_trio_wes_lftp_download.sh
diff --git a/old_submit_trio_wes_aspera_download.sh b/old_submit_trio_wes_aspera_download.sh
new file mode 100755
index 0000000..2a1221a
--- /dev/null
+++ b/old_submit_trio_wes_aspera_download.sh
@@ -0,0 +1,23 @@
+#!/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
diff --git a/submit_trio_wes_lftp_download.sh b/submit_trio_wes_lftp_download.sh
new file mode 100755
index 0000000..f7dba57
--- /dev/null
+++ b/submit_trio_wes_lftp_download.sh
@@ -0,0 +1,37 @@
+#!/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
--
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