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Preparing the environment

First, we will walk you through the basics of using the command line interface (CLI), which is essential for running tools like spacemake and Open-ST. We assume you are running Linux (e.g., Ubuntu 22.04). A computer with at least 128 GB of RAM is recommended for spacemake and openst. Future optimizations to spacemake will reduce memory requirements.

Installing dependencies

We will install two dependencies: spacemake and openst.

For this, we assume that you have installed mamba or any similar (e.g., micromamba), and you have opened a terminal (local or remote machine).

Create a new directory for this tutorial.

WORKDIR="~/openst_demo" # change this to any folder you want
mkdir -p $WORKDIR
cd $WORKDIR

During the rest of the tutorial, the root working directory will be 

~/openst_demo

Which we store in the environment variable $WORKDIR. You can change this to anything else.

Installing spacemake

Then, create a new environment for spacemake:

wget "https://raw.githubusercontent.com/rajewsky-lab/spacemake/master/environment.yaml"
mamba env create -n openst -f environment.yaml
mamba activate openst
pip install spacemake

Check that your spacemake version matches the one that will be used for this tutorial (0.7.9)

spacemake --version
# make sure it is 0.7.9 or greater

Installing openst

Now, create another environment for openst. We have developed openst separately from spacemake, because spacemake is tech-agnostic (can run on scRNA-seq, Visium, Open-ST), while openst provides tools that are specific to the Open-ST technology (for segmenting, aligning, visualizing, image pre-processing...)

# make sure the environment is still active!
# mamba activate openst
pip install openst

Check that your openst version matches the one that will be used for this tutorial (0.2.3)

openst --version
# make sure it is 0.2.3 or greater

Note

You might need to leave things running in the background (some things take hours to finish). We recommend using tmux; from the RedHat Sysadmin article:

>Tmux is a terminal multiplexer; it allows you to create several "pseudo terminals" from a single terminal.

>This is very useful for running multiple programs with a single connection,

>such as when you're remotely connecting to a machine using Secure Shell (SSH).

Open your ~/.bashrc (or ~/.zshrc) file with a text editor, or VIM, or anything else, and add the following lines:

alias ta='tmux attach -t'
alias tl='tmux ls'
alias tn='tmux new -s'

The next time you open a terminal, these aliases will be available:

  • tn pepa: create a new pseudo-terminal with name "pepa"
  • ta pepa: attaches to the pseudo-terminal called "pepa"
  • tl: lists all pseudo-terminals that are available

To deattach a pseudo-terminal, you have the keyboard shortcut Ctrl+b+d

To close a pseudo-terminal, you close all panels type exit and press Enter, or to close all at once you can use Ctrl+b+&