YuuMJ1997/EukPhylo
1
0
Fork 0
mirror of http://43.156.76.180:8026/YuuMJ/EukPhylo.git synced 2025-12-27 05:50:24 +08:00
Code Issues Packages Projects Releases Wiki Activity

Update README.md

Browse Source
This commit is contained in:
Godwin Ani 2025-03-14 14:57:02 -04:00 committed by GitHub
parent 76bc514ec9
commit f054c8e5a2
No known key found for this signature in database
GPG Key ID: B5690EEEBB952194
1 changed files with 14 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

17
README.md
View File

@ -8,11 +8,11 @@ EukPhylo is an updated version of the PhyloToL pipeline from the [Katz Lab](http
## 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
# Build the container
docker build -f Dockerfile.txt . --tag eukphylo:1
docker build -f Dockerfile.txt . --tag eukphylo
# Current command is:
@ -20,7 +20,18 @@ 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: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.