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Godwin Ani 2025-03-14 15:02:49 -04:00
parent bb32ff9768
commit 616a05348d
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Home.md

@ -13,13 +13,24 @@ We are in the process of containerizing EukPhylo with Docker, and we have starte
```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:
docker run -it \ 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=$(pwd)/input_data,dst=/Input_data \
--mount type=bind,src=$(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 that takes in an OGlist, taxonlist, and R2Gs as input. It also requires an Output folder.
```
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.