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 for part 2 can be executed with:

# 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.

⚠️ 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

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