PC SET UP FOR MAC USERS

1. PC SET UP FOR MAC USERS

Individual installs for packages that are not obtained through conda

1a) Install conda

Install through download link:

note, working for Windows: install Miniconda rather than anaconda

https://www.anaconda.com/download/

1b) Verify correct install of conda

Open the Terminal (app) and type the following command

.\miniconda3\_conda.exe create -n test

The above command is using conda to create a test environment called “test”

IF conda is correctly installed, you will see the following messsage after the command has finished running:

Channels: -defaults Platform: win-64 Collecting package metadata (repodata.json): done Solving environment: done ……………..

You will be prompted to proceed or not, type Y and Enter to proceed, and the test environment will finish loading.

If you did not see any of the above message, then conda has not installed properly and we will need to check this together

2) Install dorado

Install using dorado’s install link depending on what system you are working on:

https://github.com/nanoporetech/dorado?tab=readme-ov-file

When using dorado, you have to include the whole file path to whereever you dorado version is installed, the programme itself is within the bin folder

Now that both dorado and anaconda are installed on your system, you can use anaconda (a package manager) to create working environments with the essential programmes installed.

I have created a configuration file which contains all of the essential programmes needed for our code within the Moon lab.

This environment is called moon_code

Install all other packages through conda file

3) Download the and activate the moon_code work environment

Firstly, I will email you the appropriate configuration file (.yml)

Download this and save it locally, (I tend to create a folder in my top directory called software, and store configuration files in here)

Then execute the following command to use the configuration file and install all require packages

conda env create -f ~/PATH/TO/FILE/filename.yml

This should have a successful install message, let me know if not.

Then to check the code has installed the required environment, execute the following command:

conda activate moon_code

This should change your extension in the terminal so that it has the following order:

(moon_code)USER@PC:folder_location/

You are now working in an environment where all packages are installed.

Every time that you leave the terminal, you will need to REACTIVATE YOUR WORKING ENVIRONMENT

To reactivate your working environment, use:

conda activate moon_code

Code editors

You will probably want to download a text editor for code editting, such as Sublime text

https://www.sublimetext.com/download