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Install Guide on Windows Subsystem for Linux
Open powershell as administrator (search it in the task bar, right click, run as administrator).
Run the following command:
wsl --install -d Ubuntu
After an initial install, the Ubuntu terminal will open and finish up installing. The Ubuntu terminal will then ask you for a username - the shorter the better, and a password. The password prompt will not give an indication you are typing in it, it will just stay blank, but it is working.
Once that's done, in the Ubuntu session run:
sudo apt update && sudo apt upgrade
Congrats, you now have a working WSL Ubuntu environment (and by extension, bash and git, which will come in handy later). It should have been added to your start menu searchbar, you can find it by searching 'Ubuntu'.
Run the following commands in an WSL Ubuntu terminal session:
wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.11.0-Linux-x86_64.sh
bash Miniconda3-py39_4.11.0-Linux-x86_64.sh
The first command downloads a specific version of miniconda that I know works as of 2022. One day, it may point to a dead link and you'll have to find Miniconda yourself. But hopefully that won't be for a long time, and hopefully I'll keep this page sufficiently updated for it not to matter. The second command runs the install process, which may prompt you to confirm installation and read a license agreement.
Run one more command to do some quick configuration of our newly installed copy of Conda:
conda config --set auto_activate_base false
Run the following commands in an WSL Ubuntu terminal session, replacing *VERSION* with the appropriate version number, e.g. v1.1.0:
wget https://github.com/kew-myco/its_glue/releases/download/*VERSION*/its_glue_*VERSION*_LINUX.zip
unzip its_glue_*VERSION*_LINUX.zip
Enter into the unzipped directory via:
cd its_glue_*VERSION*_LINUX
This is the top level directory of the pipeline.
Run these commands to modify permissions on the scripts, allowing us to execute them.
chmod +x ./scripts/CREATE_ENV.sh
chmod +x ./pipe_one.trace_its.sh
chmod +x ./pipe_two.cluster_classify.sh
Finally run the following command to set up the Conda environment for the pipeline and install packages:
./scripts/CREATE_ENV.sh
CREATE_ENV.sh will have Conda install all the necessary dependencies for you in a self contained Conda environment. It seems the easiest way to ensure everyone is able to run things without having to worry about installing the specific tools the pipeline relies on. This does mean that you have to run all the scripts from within the top-level pipeline directory.
You will be prompted to confirm package installation by Conda.
All done! You're good to start using the pipeline via WSL
explorer.exe . => to find the location of the ubuntu install