Chapter 3 Installation

SpaceSequest can be installed through conda environment. We have tested the installation on Linux servers. Please ensure Conda is available on your device:

which conda
# Your conda path will be returned

Then go the directory you would like to install the pipeline ($PipelineDir in the following example), execute the scripts:

git clone https://github.com/interactivereport/SpaceSequest.git
cd SpaceSequest

# This step may take a while. Thank you for your patience
bash install.sh

# The .env will be created under the src directory
ls $PipelineDir/SpaceSequest/src/.env

#Add pipeline scripts to $PATH
vim ~/.bash_profile
PATH=$PATH:$PipelineDir/scRNASequest
# Close the vim text editor and source the file
source ~/.bash_profile

#To verify the installation, type one of the main scripts, such as:
visium

#Output:
=== Welcome to 'visium' from SpaceRequest! ===
    Please provide either a path to a folder or a config file.
    An empty config file will be created if a path to a folder is provided.