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MCView maintains a docker image with all the R and python dependencies. By default, the image starts an app with the project mounted at /project in the docker fs, but you can also use it to create projects or import datasets.

Pull the image

Pull the MCView docker image using:

docker pull tanaylab/mcview:latest

Create a project

mkdir PBMC
docker run -v $(pwd)/PBMC:/project tanaylab/mcview R -e 'MCView::create_project("/project/PBMC")'

Import a dataset

Download the PBMC example dataset:

tar xvzf PBMC_processed.tar.gz

Import the dataset:

docker run -v $(pwd):/workdir tanaylab/mcview R -e 'MCView::import_dataset("/workdir/PBMC", dataset = "PBMC163k", anndata_file = "/workdir/metacells.h5ad", cell_type_colors_file = "/workdir/cluster-colors.csv")'

Run the app

docker run -v $(pwd)/PBMC:/project -p 3838:3838 tanaylab/mcview

We can now go to port 3838 on our machine to view the running app.