millironx/sc2-sequencing
1
0
Fork 0
mirror of https://github.com/MillironX/sc2-sequencing.git synced 2024-12-22 11:18:17 +00:00
Code Issues Releases Packages Activity

Test if USB drive is inserted

Browse source
This commit is contained in:
Thomas A. Christensen II 2021-03-23 14:00:18 -06:00
parent 7c316ff08b
commit 261e1e01d6
Signed by: millironx
GPG key ID: 139C07724802BC5D
1 changed files with 6 additions and 2 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

8
ont/ont-transfer.sh
View file

@ -14,7 +14,7 @@ fi
# Find the directory we are supposed to copy # Find the directory we are supposed to copy
# If no directory was passed, check to see if the current directory will work # If no directory was passed, check to see if the current directory will work
if [ "$FOLDERIN" = "" ]; then if [[ -n "$FOLDERIN" = "" ]]; then
if [[ -n $(find . -type d -name "fast5_pass") ]]; then if [[ -n $(find . -type d -name "fast5_pass") ]]; then
FOLDERPATH="$PWD" FOLDERPATH="$PWD"
FOLDERNAME=$(basename "$PWD") FOLDERNAME=$(basename "$PWD")
@ -30,7 +30,7 @@ else
fi fi
# Calculate the FASTAs that need copied # Calculate the FASTAs that need copied
if [ ! "$OFFSET" = "1" ]; then if [[ "$OFFSET" -gt 1 ]]; then
if [[ "$OFFSET" -lt 7 ]]; then if [[ "$OFFSET" -lt 7 ]]; then
KEEPERS=(01 02 03 04 05 06) KEEPERS=(01 02 03 04 05 06)
else else
@ -48,6 +48,10 @@ fi
# Find where the flash drive is mounted # Find where the flash drive is mounted
USBDRIVE=$(mount | grep /media | awk '{print $3}') USBDRIVE=$(mount | grep /media | awk '{print $3}')
if [[ -n "$USBDRIVE" ]]; then
echo "No USB drive was detected. Exiting now."
exit 1
fi
# Prompt the users # Prompt the users
echo "Extracting FAST5/FASTQ from" "$FOLDERNAME" "to USB Device $USBDRIVE, skipping after" "$OFFSET""." echo "Extracting FAST5/FASTQ from" "$FOLDERNAME" "to USB Device $USBDRIVE, skipping after" "$OFFSET""."