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Update README.md

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Godwin Ani 2025-03-18 19:01:23 -04:00 committed by GitHub
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@ -12,7 +12,7 @@ The [docker file](https://github.com/Katzlab/EukPhylo/blob/Docker/PTL1/Dockerfil
```bash ```bash
# Build the container # Build the container
docker build -f Dockerfile.txt . --tag eukphylo docker build -f Dockerfile.txt . --tag eukphylo_one
# Current command is: # Current command is:
@ -20,18 +20,17 @@ 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 eukphylo_one
``` ```
An example for running the dockerfile that takes in an OGlist, taxonlist, and R2Gs as input. It also requires an Output folder. 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)" > :warning: Do not change the "dst=/$(path)", only change "src=$(pwd)"
``` ```
docker run -it \ 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_part1/AssembledTranscripts,dst=/Input_data \
--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_part1/Databases,dst=/EukPhylo/PTL1/Transcriptomes/Scripts/Databases \
--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/R2G,dst=/Input_data \ --mount type=bind,src=/Users/gani/phylotol_ms/Docker_part1/Output_data,dst=/Output_data \
--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/Output_data,dst=/Output_data \ eukphylo_one
eukphylo
``` ```
@ -40,15 +39,16 @@ The [docker file](https://github.com/Katzlab/EukPhylo/blob/Docker/PTL2/Dockerfil
```bash ```bash
# Build the container # Build the container
docker build -f Dockerfile.txt . --tag eukphylo docker build -f Dockerfile.txt . --tag eukphylo_two
# 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)/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=$(pwd)/input_data,dst=/Input_data \
--mount type=bind,src=$(pwd)/output_data,dst=/Output_data \ --mount type=bind,src=$(pwd)/output_data,dst=/Output_data \
eukphylo eukphylo_two
``` ```
An example for running the dockerfile that takes in an OGlist, taxonlist, and R2Gs as input. It also requires an Output folder. An example for running the dockerfile that takes in an OGlist, taxonlist, and R2Gs as input. It also requires an Output folder.
@ -59,7 +59,7 @@ docker run -it \
--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/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/R2G,dst=/Input_data \
--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/Output_data,dst=/Output_data \ --mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/Output_data,dst=/Output_data \
eukphylo eukphylo_two
``` ```