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<img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/Katzlab.png">
**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.