EukPhylo is an updated version of the PhyloToL pipeline from the Katz Lab at Smith College. EukPhylo is a phylogenomic toolkit for processing transcriptomic and genomic data that includes novel phylogeny-informed contamination removal techniques. See our Wiki for more information on installation and usage!

Dockerfile

The docker file can be executed with:

cd EukPhylo

# Build the container
docker build -f Dockerfile . --tag MyEuk:1

# Get the container IMAGE_ID
docker image list

# Current command is:
docker run -it \
    --mount type=bind,src=$(pwd)/databases,dst=/Databases \
    --mount type=bind,src=$(pwd)/input_data,dst=/Input_data \
    --mount type=bind,src=$(pwd)/output_data,dst=/Output_data \
    {IMAGE_ID}

After development, GitHub CICD workflows can be added to automatically build and release the dockerfile for the end user.