You can transfer your files from your hard drive to your instance using an SCP ciient. WinSCP is a popular suggestion for Windows users, and FileZilla for MacOS/Linux. There are lots of guides on the specifics, but generally, the only stumbling blocks are realising that the “host address” is the IP address of your instance, and the username will be “ubuntu” if you are using GVL.
When you’ve transferred your files to your instance and setup SMRTPortal as per the link above, you will need to move your files into a directory that can be read/written by the
smrtanalysis user. You can accomplish this by using
sudo mv /home/ubuntu/pacbio_sequencing_files /mnt/galaxy/home/smrtanalysis
Then making sure to change the ownership of these files using
sudo chown -R smrtanalysis:smrtanalysis /mnt/galaxy/home/smrtanalysis
You should then be able to continue the above tutorial from part 3b.