Docker image for PhyloProfile tool.

Run the following command to download (if necessary) and start the PhyloProfile Docker container:

docker run --platform linux/amd64 -p 8080:80 trvinh/phyloprofile

Then open web browser and start PhyloProfile tool using this address: localhost:8080

You can mount your local taxonomy data folder into the container so that the app can use it:

docker run --platform linux/amd64 \
  -v /your/data/folder:/srv/shiny-server/data \
  -p 8080:80 \
  trvinh/phyloprofile

NOTE: Ensure that your mounted folder contains a preProcessedTaxonomy.txt file. You can generate this file using the generated_taxonomy.R script located in the app folder

Rscript app/generate_taxonomy.R /your/data/folder

1. Find the Container ID

docker ps

Example output:

CONTAINER ID   IMAGE                    COMMAND                  PORTS               NAMES
b1150680c119   trvinh/phyloprofile      "/usr/bin/shiny-serv…"   0.0.0.0:8080->80    phyloprofile_app

2. Copy Files from Host to Container

docker cp /your/data/folder/. <container_id>:/srv/shiny-server/data/

IMPORTANT: Make sure /your/data/folder contains all (and only) the following files:

• idList.txt
• preCalcTree.nw
• rankList.txt
• taxonomyMatrix.txt
• newTaxa.txt
• taxonNamesReduced.txt

1. Clone or fork this repo

git clone https://github.com/trvinh/PhyloProfileDocker.git

2. Update the app folder reflect the latest version of (PhyloProfile)(https://github.com/BIONF/PhyloProfile)
3. Update Docker-specific files: edit the Dockerfile as needed (for example, to update the version of the bioconductor/bioconductor_docker base image)
4. (OPTIONAL) Pre-generate preProcessedTaxonomy.txt to save time during image build

Rscript app/generate_taxonomy.R app/data

5. Build the docker image

docker build . -t trvinh/phyloprofile[:1.20.4] --platform linux/amd64 --progress=plain

Note: you need to replace trvinh by your Docker Username. :0.1.2 specifies the TAG of your build (if empty, the default tag latest will be applied)

6. Push to Docker Hub

docker push trvinh/phyloprofile[:1.20.4]

7. Clean build caches after pushing

Use this command to see how large is the cache

docker system df

and run this to free the disk space

docker buildx prune

Check this document for more info!

8. (OPTIONAL) Inspect the shiny server

docker run --platform linux/amd64 -it --rm --entrypoint /bin/bash trvinh/phyloprofile