Setting and Customizing OT-2 for LAP Entries

Creation ssh-key connection

An OT-key should be generated to connect to the robot, and it is done with the ssh-keygen command and transferring the public key to the OT.

For more information about how to generate and set the connection between your computer and the Opentrons robot, visit https://support.opentrons.com/s/article/Setting-up-SSH-access-to-your-OT-2

Connect to the robot

To connect to the robot's system to perform different actions such as installing packages, check files that are in the system, etc.

Find the IP of the robot

In the OT app go to Devices -> Robot you want to connect -> Superior 3 dots -> Robot Settings -> Networking

Connect to the robot

Either in a bash (unix systems) or powershell (windows systems) use the command ssh

#Connect to Linux based OT via ssh 
ssh -i [path ot_key] root@[Robot_IP]

Citation

Connect to the robot

You can either connect on the same inalambric network as the robot or by USB

Find the IP of the robot

Transfer the files

In different systems you can/must transfer the files in different ways always taking in account that the system of the OT-2 robot is a Linux Raspberry

MacOS/Linux

We can use the bash or command line to transfer the file(s) with the following command

#Passing Files to OT 
scp -i [ot_key] [file_to_send] root@[IP_OT]:[final_path]
```The ot_key is referring to the private key created in step 1,  





You can face difficulties transferring files in MacOS Ventura (13) and Sonoma (14). These problems can be solved by adding the argument -O (uppercase o) to the command

#Transferring files to OT (MacOS 13 and 14) scp -O -i [ot_keypath] [file path to send] root@[IP_robot]:[final_path]

Windows

There are several ways to send files from a Windows to a Linux system (for example, with a virtual machine or Windows Powershell in the latest versions of Windows). With the latter you can use the same steps as in 5.1

Another way is using FileZilla (https://filezilla-project.org/download.php?type=client).

You can set the connection between your computer and the OT-2 robot system as follows.

Open Filezilla -> File (in the toolbar) -> Site Manager -> New Site (Press button) -> Rename Site

Now that the site is created you can see on the right the settings of that particular site. In the General tab Change Protocol to SFTP . Then, introduce in Host the OT IP, change the Logon Type to key file , change User to root and give the directory where the OT key is. It should look something like the following image

Then press Connect , and we will have a connection between our computer and the robot.

After this connection, we should be able to move the files that we want to the final path of the robot that we desire to send them.

This method can be used as well in some Linux and MacOS systems

Exit the robot

To return to your system you only need to type exit in the command line

Check needed packages and versions of LAP entry

In the Requirements Section of each LAP Entry you can find that the protocol/entry needs more packages than the ones are installed in the OT-2 system

Check python packages of robot

To know which packages are needed to be installed in the opentrons robot you can connect to the robot ()and get a list of all the packages and their versions installed in that scpecific python

Take in account that there are some packages like math or random which versions are specified or linked to the python version

Connect to robot

Use pip command

You can use the pip command to get the entire packages that are installed in your robot's version of python. Take in account that the packages that are by default in python such as math will not appear in that list

#List installed pip packages (Unix)
pip list
```To store the packages of the robot in a file for the future you can use the pipe > 

#List installed pip packages and save (Unix) pip list > [name_file_store_packages]

You can check for a specific package with the following command

#List installed pip specific package (Unix) pip show [name_package]

1. A small piece of text giving you the name, version and summary of the package, within other information. This will mean that the package is installed on the python
1. Warning message telling you that the package does not exist. This means that either the package has not been installed in that version of python or that it is not installed with pip (it is by default in python or it is installed with other vias like conda)

Install needed packages

To install 1 or more packages you can use any of the following 2 commands

#Install package Python 
python -m pip install [name_package_1] [name_package_2] [name_package_3]

#Install packages with pip 
pip install [name_package_1] [name_package_2] [name_package_3]
```Make sure that the robot has access to the internet so it can download the packages



<Note title="Note" type="warning" ><span>For more information about installing packages in the opentrons robots, check the following Opentrons page: <b>For more information about installing packages in the opentrons robots, check the following Opentrons page: https://support.opentrons.com/s/article/Using-Python-packages-in-Python-API-protocols</b></span></Note>

Exit the robot

To return to your system you only need to type exit in the command line

Creation of .json custom labware file

The description file can be obtained by describing the labware dimensions at https://labware.opentrons.com/create/

Uploading file to the OT App

In the OT app, we need to perform the following route: Labware -> Import -> Choose File -> Select file we have created in step 9

In some LAP entries or in versions of them there is a need to upload in 2 places the created files so you need to complete as well the following steps.

Uploading definition to OT robot system

Create a directory with the defintion

We need to create a directory with the API name of the labware, the name that we are going to use to load it in the opentrons

Rename .json file

We need to rename the .json file that the opentrons labware creation to 1.json and place it inside of the directory created in Step 13.1

Transfer the directory to a specific location

To upload the directory with the .json file that represents the custom labware that has been created in step 11 to the robot systems we are going to use the steps from 3 to 6 transferring the file to the final path /data/labware/v2/custom_definitions/custom_beta with some changes with the argument -r as shown in the following command

#Transferring the used custom labware to OT (Linux)
scp -i [ot_key] -r [custom labware directory path] root@[IP_OT]:/data/labware/v2/custom_definitions/custom_beta
```You can face difficulties transferring files in MacOS Ventura (13) and Sonoma (14). These problems can be solved by adding the argument -O (uppercase o) to the command

#Transferring the used custom labware to OT (Linux) scp -O -i [ot_key] -r [custom labware directory path] root@[IP_OT]:/data/labware/v2/custom_definitions/custom_beta