Step 1: Install Zorn
Zorn is under active development, so just get it straight from GitHub and install from source:
if (!requireNamespace("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github("henriksson-lab/zorn")You can then load it:
Step 2: Install Bascet
You also need Bascet, our command-line suite for single-cell analysis. Most users will find it easiest to run Bascet through Singularity or Docker; instructions for each are described below. Singularity is for Linux users, while OSX and Windows users have to use Docker.
Install Bascet via Singularity (Linux only)
First install Singularity.
Note one possibly annoying default setting! We could not read Bascet files on some file systems, because they were invisible to Bascet. To avoid this, edit /etc/singularity/singularity.conf to below:
mount hostfs = yesOnce installed, Zorn can then pull down the latest Singularity image for you. We recommend keeping it in a separate directory from your workspace, as multiple workspaces can share the same image
bascetInstance.default <- getBascetSingularityImage(storeAt="/somewhere/on/your/disk/")Install Bascet via Docker (Singularity is recommended for Linux)
First install Docker.
Once installed, Zorn can then pull down the latest Docker image for you. We recommend keeping it in a separate directory from your workspace, as multiple workspaces can share the same image
bascetInstance.default <- getBascetDockerImage(storeAt="/somewhere/on/your/disk/")Step 3: Test the installation
Run the following and see if you get “ok” before proceeding:
TestBascetInstance(bascetInstance.default)Using the Bascet instance
You need to pass the bascet_inst variable to each Zorn command that requires it. The singularity image will be cached, so if you run this again, it will instead use the previous image. You will need to delete it manually if you wish to replace it.