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67 lines
2.8 KiB
Markdown
67 lines
2.8 KiB
Markdown
<img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/Katzlab.png">
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> :warning: ** This is currently being dockerised! ** Use the container at your own peril!
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# **EukPhylo version 1.0**
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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!
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## Dockerfile
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The [docker file](https://github.com/Katzlab/EukPhylo/blob/Docker/PTL1/Dockerfile.txt) for part 1 can be executed with:
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```bash
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# Build the container
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docker build -f Dockerfile.txt . --tag eukphylo_one
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# Current command is:
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docker run -it \
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--mount type=bind,src=$(pwd)/databases,dst=/Databases \
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--mount type=bind,src=$(pwd)/input_data,dst=/Input_data \
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--mount type=bind,src=$(pwd)/output_data,dst=/Output_data \
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eukphylo_one
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```
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An example for running the dockerfile that takes in an OGlist, taxonlist, and R2Gs as input. It also requires an Output folder.
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> :warning: Do not change the "dst=/$(path)", only change "src=$(pwd)"
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```
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docker run -it \
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--mount type=bind,src=/Users/gani/phylotol_ms/Docker_part1/AssembledTranscripts,dst=/Input_data \
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--mount type=bind,src=/Users/gani/phylotol_ms/Docker_part1/Databases,dst=/EukPhylo/PTL1/Transcriptomes/Scripts/Databases \
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--mount type=bind,src=/Users/gani/phylotol_ms/Docker_part1/Output_data,dst=/Output_data \
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eukphylo_one
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```
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The [docker file](https://github.com/Katzlab/EukPhylo/blob/Docker/PTL2/Dockerfile.txt) for part 2 can be executed with:
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```bash
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# Build the container
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docker build -f Dockerfile.txt . --tag eukphylo_two
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# Current command is:
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docker run -it \
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--mount type=bind,src=$(pwd)/OG_list.txt,dst=/EukPhylo/PTL2listofOGs.txt \
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--mount type=bind,src=$(pwd)/taxon_list.txt,dst=/EukPhylo/PTL2taxon_list.txt \
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--mount type=bind,src=$(pwd)/input_data,dst=/Input_data \
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--mount type=bind,src=$(pwd)/output_data,dst=/Output_data \
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eukphylo_two
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```
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An example for running the dockerfile that takes in an OGlist, taxonlist, and R2Gs as input. It also requires an Output folder.
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> :warning: Do not change the "dst=/$(path)", only change "src=$(pwd)"
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```
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docker run -it \
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--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/OG_list.txt,dst=/EukPhylo/PTL2listofOGs.txt \
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--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/taxon_list.txt,dst=/EukPhylo/PTL2taxon_list.txt \
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--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/R2G,dst=/Input_data \
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--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/Output_data,dst=/Output_data \
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eukphylo_two
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```
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After development, GitHub CICD workflows can be added to automatically build and release the dockerfile for the end user.
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