TLC-MS_manager installation

The TLC-MS_manager is an open-source software to control the autoTLC-MS interface.

There are four options to install the TLC-MS_manager as follows.

Ubuntu 18.04.5 LTS image for a NUC PC

Follow this link to download an image of Ubuntu 18.04.5 with the installed TLC-MS_manager, last updated: 2021-02-10 (3.7 GB), and copy it onto an USB stick.

Higher versions of Ubuntu cannot be used, because some needed libraries are not available for Ubuntu >18.

To flash the image, boot the NUC from DVD (Ubuntu 18.04.5 LTS) (Live-CD).

• Therefore, download Ubuntu 18 (https://releases.ubuntu.com/18.04/) and flash the ISO onto a DVD.
• Attach the DVD to the NUC and start the PC. On booting select "Try Ubuntu without installation" and wait for the booting process.
• Attach the USB stick with the downloaded image file (TLCMS_Ubuntu18.gz).
  
• Open a terminal and type:
• sudo fdisk -l to identify the NUC-SSD (typically /dev/sda) and the USB stick (typically /dev/sdb).
  
• With df -l the information is given, under which name the USB stick is mounted, for example /media/ubuntu/NAME.
• Unmount the SSD: sudo umount /dev/sda followed by sudo su, to get root privileges
  
• Start flashing with:
  cat /media/ubuntu/NAME/TLCMS_Ubuntu18.gz | gunzip -d -c | dd of =/dev/sda bs=32k.
  
• After finishing, check the values of 'in' and 'out', which should be fully identical, if nothing went wrong.
  
• Reboot the NUC while detaching the DVD on command.
• User name: pi, password: tlcms
• Configure Ubuntu for your purposes (language, keyboard).
• Configure a proper time server:

sudo nano /etc/systemd/timesyncd.conf

"edit the line fallbackNTP= ... followed by"

sudo timedatectl set-ntp true
sudo reboot

• After date and time is correctly synchronized, perform update und upgrade:

sudo apt update
sudo apt upgrade

Alternatively, manual installation of TLC-MS_manager on a NUC PC with Ubuntu 18.04.5 LTS already installed, using the installation script

First install the git library:

sudo apt install git

Then clone this github repository:

git clone https://github.com/OfficeChromatography/TLC-MS_manager.git

Installation

In the downloaded folder home/TLC-MS_manager, there is an installation script (TLC-MS_manager_Ubuntu-18-04_install.sh) to be executed (last updated and tested 2021-02-10). Therefore, open the file sudo_bash.txt, and copy the repective command line into the terminal.

In case of installation problems, the log file TLC-MS_manager-Ubuntu_install.txt (in home/) can be checked for error messages concerning, for example, missing dependencies.

Raspberry Pi OS image

Follow this link to download an image of a Raspberry Pi OS with the installed TLC-MS_manager, last updated 2021-02-10 (2.1 GB).

• Flash the image onto an SD card (>= 16 GB), best using the Raspberry Pi Imager (https://www.raspberrypi.org/software/).
• Insert the SD card into the Raspberry Pi 4B with 4 GB RAM and boot the system.
• Configure the Raspberry Pi for your purposes (language, keyboard).
• User name: pi, password: tlcms
• Configure a proper time server:

sudo nano /etc/systemd/timesyncd.conf

"edit the line fallbackNTP= ... followed by"

sudo timedatectl set-ntp true
sudo reboot

• After date and time is correctly synchronized, perform update und upgrade:

sudo apt-get update
sudo apt-get upgrade

Alternatively, manual installation of TLC-MS_manager on a Raspberry Pi 4B with an OS already installed, using the installation script

There is a different installation script for the Raspberry Pi in the downloaded folder home/pi/TLC-MS_manager. Use the respective sudo bash command to be found in the file sudo_bash.txt.

Unfortunately, the new Ubuntu 20.10 OS for the Raspberry Pi 4B does not work, because some needed libraries are not available for this OS.

Starting the TLC-MS_manager

Starting at reboot with crontab

Crontab is a job scheduler for UNIX-like system. The file can be accessed with the following command and the lines inside will be executed at the appropriate moment.

sudo crontab -e

Once in the editor, add this line for both the NUC and Raspberry Pi:

@reboot Rscript /home/pi/TLC-MS_manager/app_exec.R

After reboot, the TLC-MS_manager will be available in the browser at http://127.0.0.1 (localhost).
Therefore, best configure the browser to start with the custom URL http://127.0.0.1/.

If a static IP had been set, the application will also be available at the IP (in the browser) from a remote computer in the network.

Starting directly from R (in case of problems to catch the errors)

Being in a terminal:

cd TLC-MS_manager

R

shiny::runApp()

Documentation

An instruction manual (pdf) is available in the downloaded folder TLC-MS_manager/Instruction.

The same instruction manual is also available in the "Read me" tab of the TLC-MS_manager software.