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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
# Build the container
docker build -f Dockerfile.txt . --tag eukphylo
docker build -f Dockerfile.txt . --tag eukphylo_one
# Current command is:
@ -20,18 +20,17 @@ 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=$(pwd)/output_data,dst=/Output_data \
eukphylo
eukphylo_one
```
An example for running the dockerfile that takes in an OGlist, taxonlist, and R2Gs as input. It also requires an Output folder.
> :warning: Do not change the "dst=/$(path)", only change "src=$(pwd)"
```
docker run -it \
--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/OG_list.txt,dst=/EukPhylo/PTL2listofOGs.txt \
--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/taxon_list.txt,dst=/EukPhylo/PTL2taxon_list.txt \
--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/R2G,dst=/Input_data \
--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/Output_data,dst=/Output_data \
eukphylo
--mount type=bind,src=/Users/gani/phylotol_ms/Docker_part1/AssembledTranscripts,dst=/Input_data \
--mount type=bind,src=/Users/gani/phylotol_ms/Docker_part1/Databases,dst=/EukPhylo/PTL1/Transcriptomes/Scripts/Databases \
--mount type=bind,src=/Users/gani/phylotol_ms/Docker_part1/Output_data,dst=/Output_data \
eukphylo_one
```
@ -40,15 +39,16 @@ The [docker file](https://github.com/Katzlab/EukPhylo/blob/Docker/PTL2/Dockerfil
```bash
# Build the container
docker build -f Dockerfile.txt . --tag eukphylo
docker build -f Dockerfile.txt . --tag eukphylo_two
# Current command is:
docker run -it \
--mount type=bind,src=$(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)/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.
@ -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/R2G,dst=/Input_data \
--mount type=bind,src=/Users/gani/phylotol_ms/Docker/PT2/Output_data,dst=/Output_data \
eukphylo
eukphylo_two
```