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@ -8,6 +8,34 @@ EukPhylo is an updated version of the PhyloToL pipeline from the [Katz Lab](http
## Dockerfile
The [docker file](https://github.com/Katzlab/EukPhylo/blob/Docker/PTL1/Dockerfile.txt) for part 1 can be executed with:
```bash
# Build the container
docker build -f Dockerfile.txt . --tag eukphylo
# 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=$(pwd)/output_data,dst=/Output_data \
eukphylo
```
An example for running the dockerfile that takes in an OGlist, taxonlist, and R2Gs as input. It also requires an Output folder.
> :warning: Do not change the "dst=/$(path)", only change "src=$(pwd)"
```
docker run -it \
--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/OG_list.txt,dst=/EukPhylo/PTL2listofOGs.txt \
--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/taxon_list.txt,dst=/EukPhylo/PTL2taxon_list.txt \
--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/R2G,dst=/Input_data \
--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/Output_data,dst=/Output_data \
eukphylo
```
The [docker file](https://github.com/Katzlab/EukPhylo/blob/Docker/PTL2/Dockerfile.txt) for part 2 can be executed with:
```bash