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Stand-alone Guppy on MinIT
To install and run Guppy on MinIT, you can consult the Guppy protocol once support is provided.
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Changing output directory - SSH
All output is written to
/data
by default which is located on the internal SSD of the MinIT.If you plug in a USB hard drive, it should be available via
/media/usb
The output directories can be changed. To change the output directory:
Edit the MinKNOW configuration file:
sudo vim /opt/ONT/MinKNOW/conf/user_conf
Change the output directory file - you should change base from
/data
to if you only want the data to move from the dirs to different media.Restart the MinIT
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Data transfer - SSH - Windows
To move files on and off the MinIT, you can use the
pscp
command. You can do this by following the instructions below:- Enter the terminal.
- Enter the
pscp
command as detailed in the excerpt from www.ssh.com, using the MinIT server and hostname (e.g.minit@mt-100007), file name, its directory, the directory you wish to copy to.
To receive a file from a server:
pscp [options] [user@]host:source target
So to copy the file/etc/hosts
from theserver example.com
as userfred
to the file >c:\temp\example-hosts.txt
, you would type:
pscp fred@example.com:/etc/hosts c:\temp\example-hosts.tx
e.g.
minit@mt-100007:/data/basecalled data [full directory path you wish to copy the file to]
Note: For more help, follow the instructions for PuTTY
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Data transfer - SSH - macOS/Linux
- Open a terminal window
Connect to the machine using the
sftp
command below.
sftp -o ServerAliveInterval=10 -o TCPKeepAlive=no -i /Users/$(whoami)/Downloads/[Device Name]
To input the path to file you wish to move, simply drag the file onto to the terminal window. This path may be different than above depending on where you saved the file.
Once connected download the script output files with the get command:
sftp> get [File Name]
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Log files transfer - SSH
The logs record the command-line information that the MinIT is using to run MinKNOW, the Admin interface and the operating system, Linux.
These records can be used by Technical Support at Oxford Nanopore Technologies to diagnose errors and crashes that occur on users' MinITs.
To access these files using the terminal/SSH, follow the commands here and in Data transfer - SSH sections.
- Open a terminal
- Login, if you have not already done so, using
pscp
orsftp
and username:minit
and password:minit
. - Using the relevant commands for
sftp
orpscp
, copy over the file/var/log/MinKNOW
to your computer/laptop. - You will then find your logs in the location identified in the file transfer command.