diff --git a/ont/ont-transfer.sh b/ont/ont-transfer similarity index 80% rename from ont/ont-transfer.sh rename to ont/ont-transfer index 77112c8..9103b45 100755 --- a/ont/ont-transfer.sh +++ b/ont/ont-transfer @@ -14,7 +14,7 @@ fi # Find the directory we are supposed to copy # If no directory was passed, check to see if the current directory will work -if [[ -n "$FOLDERIN" = "" ]]; then +if [[ ! -n "$FOLDERIN" ]]; then if [[ -n $(find . -type d -name "fast5_pass") ]]; then FOLDERPATH="$PWD" FOLDERNAME=$(basename "$PWD") @@ -30,16 +30,16 @@ else fi # Calculate the FASTAs that need copied -if [[ "$OFFSET" -gt 1 ]]; then - if [[ "$OFFSET" -lt 7 ]]; then +if [[ $OFFSET -gt 1 ]]; then + if [[ $OFFSET -lt 7 ]]; then KEEPERS=(01 02 03 04 05 06) else KEEPERS=(07 08 09 10 11 12) fi for ((i = 1; i < 8; ++i)); do - WORKING=("${KEEPERS[@]: -6}") + WORKING=(${KEEPERS[@]: -6}) for ((j = 0; j < 6; ++j)); do - KEEPERS+=($(("${WORKING[j]}" + 12))) + KEEPERS+=($(( 10#${WORKING[j]} + 12 ))) done done else @@ -47,14 +47,15 @@ else fi # Find where the flash drive is mounted -USBDRIVE=$(mount | grep /media | awk '{print $3}') -if [[ -n "$USBDRIVE" ]]; then +# Note that this only works on GridIONs thanks to goofy mounting +USBDRIVE=$(mount | grep /data | awk '{print $3}' | tail -n1) +if [[ -n $(echo $USBDRIVE | grep scratch) ]]; then echo "No USB drive was detected. Exiting now." exit 1 fi # Prompt the users -echo "Extracting FAST5/FASTQ from" "$FOLDERNAME" "to USB Device $USBDRIVE, skipping after" "$OFFSET""." +echo "Extracting FAST5/FASTQ from $FOLDERNAME to USB Device $USBDRIVE, skipping after $OFFSET." echo "If this is not correct, press CTRL+C within the next 10 seconds to abort..." sleep 10 echo "Proceeding..." @@ -64,7 +65,7 @@ mkdir -p "$USBDRIVE/$FOLDERNAME/fast5" mkdir -p "$USBDRIVE/$FOLDERNAME/fastq" # Copy the files -for FASTA in "${KEEPERS[@]}"; do +for FASTA in ${KEEPERS[@]}; do cp -n $FOLDERPATH/*/fast5_pass/barcode$FASTA/*.fast5 $USBDRIVE/$FOLDERNAME/fast5 2> /dev/null cp -n $FOLDERPATH/*/fastq_pass/barcode$FASTA/*.fastq $USBDRIVE/$FOLDERNAME/fastq 2> /dev/null cp -n $FOLDERPATH/*/fastq_pass/barcode$FASTA/*.fastq.gz $USBDRIVE/$FOLDERNAME/fastq 2> /dev/null