Nanopore_rsync

Live sync basecalled Nanopore reads from computer running the MinION to a server or location of your choice.

Installing rsync: YOU MUST INSTALL "rsync" AND ADD IT TO YOUR PATH ON BOTH THE LOCAL AND DESTINATION MACHINES FOR THIS TO WORK.

Installing rsync on Mac (using homebrew):

Install Homebrew. Here is a link to their website for reference... you dont need to go here (https://brew.sh).

Open Terminal

and type the following after the prompt

$ /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Install rsync

$ brew install rsync

link rsync

$ brew link rsync

Test rsync to see if it was installed and is accessible

$ which rsync

You should see something like this

$ which rsync usr/bin/rsync

To view the rsync documentation type

$ rsync -h

Using Nanopore_rsync

Save Nanopore_rsync to your desktop.

Navigate to your desktop in terminal

$ cd ~/Desktop

Make sure that Nanopore_rsync is executable

$ chmod +x Nanopore_rsync

Now we will add your source and destination directories. The syntax for this is as follows:

$ rsync /path/to/target /path/to/destination

Using a text editor specify your source folder (the location to which MinKNOW saves its .fast5 or .fastq read files)

The default is /path/to/source

You need to edit this to your source folder like the following example /Library/MinKNOW/data/reads/20170526_2032_Run6_5_26_2016_FAH04563/fastq/pass

Using a text editor specify your destination folder (the location to which you would like to copy your nanopore output)

The default is /path/to/destination

You need to edit this to your destination folder like the following example /Volumes/MORL/Analysis/ranum/Nanopore/Run6

After entering your destination folder save the Nanopore_rsync document.

Now you are ready to run Nanopore_rsync

$ bash Nanopore_rsync

This script was created to work on Mac computers which save MinION basecalled reads to /Library/MinKNOW/data/reads/pass

It utilizes the rsync package using the recursive (-r) and time (-t) flags allowing it to sync files in sub directories and to prompted to re-run every 30 minutes (1800).

This pretty much covers it. Happy poreing.

• Paul Ranum