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Godwin Ani 2025-03-14 14:57:02 -04:00 committed by GitHub
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@ -8,11 +8,11 @@ EukPhylo is an updated version of the PhyloToL pipeline from the [Katz Lab](http
## Dockerfile ## Dockerfile
The docker file can be executed with: The [docker file](https://github.com/Katzlab/EukPhylo/blob/Docker/PTL2/Dockerfile.txt) for part 2 can be executed with:
```bash ```bash
# Build the container # Build the container
docker build -f Dockerfile.txt . --tag eukphylo:1 docker build -f Dockerfile.txt . --tag eukphylo
# Current command is: # Current command is:
@ -20,7 +20,18 @@ docker run -it \
--mount type=bind,src=$(pwd)/databases,dst=/Databases \ --mount type=bind,src=$(pwd)/databases,dst=/Databases \
--mount type=bind,src=$(pwd)/input_data,dst=/Input_data \ --mount type=bind,src=$(pwd)/input_data,dst=/Input_data \
--mount type=bind,src=$(pwd)/output_data,dst=/Output_data \ --mount type=bind,src=$(pwd)/output_data,dst=/Output_data \
eukphylo:1 eukphylo
``` ```
An example for running the dockerfile
```
docker run -it \
--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/PTL2listofOGs.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. After development, GitHub CICD workflows can be added to automatically build and release the dockerfile for the end user.