> :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](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_one # 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=$(pwd)/output_data,dst=/Output_data \ eukphylo_one ``` An example for running the dockerfile that takes in an OGlist, taxonlist, and R2Gs as input. It also requires an Output folder. > :warning: Do not change the "dst=/$(path)", only change "src=$(pwd)" ``` docker run -it \ --mount type=bind,src=/Users/gani/phylotol_ms/Docker_part1/AssembledTranscripts,dst=/Input_data \ --mount type=bind,src=/Users/gani/phylotol_ms/Docker_part1/Databases,dst=/EukPhylo/PTL1/Transcriptomes/Scripts/Databases \ --mount type=bind,src=/Users/gani/phylotol_ms/Docker_part1/Output_data,dst=/Output_data \ eukphylo_one ``` The [docker file](https://github.com/Katzlab/EukPhylo/blob/Docker/PTL2/Dockerfile.txt) for part 2 can be executed with: ```bash # Build the container docker build -f Dockerfile.txt . --tag eukphylo_two # Current command is: docker run -it \ --mount type=bind,src=$(pwd)/OG_list.txt,dst=/EukPhylo/PTL2listofOGs.txt \ --mount type=bind,src=$(pwd)/taxon_list.txt,dst=/EukPhylo/PTL2taxon_list.txt \ --mount type=bind,src=$(pwd)/input_data,dst=/Input_data \ --mount type=bind,src=$(pwd)/output_data,dst=/Output_data \ eukphylo_two ``` An example for running the dockerfile that takes in an OGlist, taxonlist, and R2Gs as input. It also requires an Output folder. > :warning: Do not change the "dst=/$(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_two ``` After development, GitHub CICD workflows can be added to automatically build and release the dockerfile for the end user.