-
From MinKNOW version 21.02 onwards, we have added new functionality to enable smoother data transfer off the box during a sequencing run. The instructions below are an example method to mount an external NFS and transfer data. Please consult your local IT department before implementing any code to ensure it is compatible with the local infrastructure and the correct permissions are in place.
-
Mount your local NFS file system on the device (note that Linux mounts a remote filesystem into a directory locally). Below is an example setup through the terminal:
prom@PCT0001:~$ sudo su -
prom@PCT0001:~$ apt install autofs
prom@PCT0001:~$ echo -en “+auto.master\n/nfs /etc/auto.ont\n” > /etc/auto.master
prom@PCT0001:~$ echo -en "NETWORKSTORAGE -nfsvers=3,rw,bg,async,actimeo=300,soft,intr,noatime,tcp,nolock IPADDRESS:/PATH/TO/SHARE" > /etc/auto.ont
prom@PCT0001:~$ ln -s /nfs/NETWORKSTORAGE /media/NETWORKSTORAGE
prom@PCT0001:~$ ls -al /media/NETWORKSTORAGE/*
-
Install the latest version of the MinKNOW software:
prom@PCT0001:~$ sudo apt update
prom@PCT0001:~$ sudo apt install ont-promethion-release
-
Make a source directory that your experiments will be saved to in /data/ , for example:
prom@PCT0001:~$ mkdir /data/data-offload
-
Make a destination directory on your networked storage. This also tests that the ‘prom’ user can write to the networked storage:
prom@PCT0001:~$ mkdir /media/mounted_drive/destination_directory/
-
As root, edit /etc/systemd/ont-platform-data-offload.conf to set the SOURCE_DIR and DESTINATION_DIR variables. SOURCE_DIR is the directory the PromethION software writes to, and DESTINATION_DIR is on your networked storage.
prom@PCT0001:~$ sudo vi /etc/systemd/ont-platform-data-offload.conf
-
A log of the actions taken by the script will be written to /data/data-offload.log
-
Start your sequencing in the MinKNOW UI, setting the output location to SOURCE_DIR set above.
-
We currently recommend manually controlling the service, as the data offload activity could affect active runs.
To start the offload service as root:
sudo systemctl start ont-platform-data-offload
To stop the offload service as root:
sudo systemctl stop ont-platform-data-offload
-
To check that the service is running, run the following command:
sudo systemctl status ont-platform-data-offload