fast5upload

fast5upload is a tool that works with MinKNOW to automatically upload your sequenced raw data to our server for further data analyses, basecalling included.

Installation

Prerequisite

We assume that you have finished following the MinKNOW manual to install it onto an Ubuntu 22.04 machine. You also have an active Internet connection during setup, as well as during actual run.

Download the package

You may obtain the latest version of the package from the following URL:

• https://mlstverse.org/release/fast5upload_latest.deb

Install the package

We recommend using apt to complete the installation, so that the libraries this program depends on could be installed automatically as well.

sudo apt install ~/Downloads/fast5upload_latest.deb

Basic configurations

Before you can use this tool, you would need to tell it your login information.

sudo gedit /etc/mlstverse/fast5upload.conf

With the opened editor window, please fill in the blanks of "user" and "password". Save the file, and test your setup.

sudo fast5upload-debug

This program would output a few information regarding your current setup. If you see your account name being Welcomed, and You are good to go at the end, your configuration is working.

If anything went wrong during such test, please contact us with a copy of the output for further help.

Enable fast5upload service

This tool is managed by systemd. To use it only for certain runs, execute the following command before and after the run:

systemctl start fast5upload

# Run your sequencer

systemctl stop fast5upload

If you do not want to start and stop it every time you have a new run, and just want to upload everything you have to us for analyses, you may instead enable this service and forget about it till next update. Use the following command to enable the service:

systemctl enable --now fast5upload