diff --git a/README.md b/README.md index e6f502c..f063f52 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,30 @@ - -**EukPhylo version 1.0** is an updated version of the PhyloToL pipeline from the [Katz Lab](https://www.science.smith.edu/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](https://github.com/Katzlab/EukPhylo/wiki) for more information on installation and usage! +> :warning: ** This is currently being dockerised! ** Use the container at your own peril! + +# **EukPhylo version 1.0** +EukPhylo is an updated version of the PhyloToL pipeline from the [Katz Lab](https://www.science.smith.edu/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](https://github.com/Katzlab/EukPhylo/wiki) for more information on installation and usage! + + +## Dockerfile + +The docker file can be executed with: + +```bash +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.