This Docker image combines two matrices using the intersection of rows

For gene expression files, columns represent subjects and rows represent genes

The output is a .csv file with the intersection of genes and all columns from both files

To execute in the command line, use:

Rscript combine_matrices.R --m1="path/to/file1" --m2="path/to/file2"

Build a Container for the combine-matrices-docker

Steps to build this docker container.

Set up GitHub Actions To build your image from the command line:

Can do this on Google shell - docker is installed and available

docker build -t combine-matrices .

To test this tool from the command line

Set up an environment variable capturing your current command line:

PWD=$(pwd)

Then mount and use your current directory and call the tool now encapsulated within the environment.

docker run -it -v $PWD:$PWD -w $PWD combine-matrices Rscript yourname.R