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31 lines
1.1 KiB
Markdown
31 lines
1.1 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 can be executed with:
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```bash
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cd EukPhylo
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# Build the container
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docker build -f Dockerfile . --tag MyEuk:1
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# Get the container IMAGE_ID
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docker image list
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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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{IMAGE_ID}
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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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