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Docker Installation

Containerized usage is recommended when you want a reproducible environment with Perl dependencies preinstalled.

Method 1: From Docker Hub​

Download the latest image from Docker Hub:

docker pull manuelrueda/convert-pheno:latest
docker image tag manuelrueda/convert-pheno:latest cnag/convert-pheno:latest

Method 2: Build From Dockerfile​

The repository includes a docker/Dockerfile.

Build the image locally with:

docker buildx build -t cnag/convert-pheno:latest .

Run The Container​

Start a detached container:

docker run -tid -e USERNAME=root --name convert-pheno cnag/convert-pheno:latest

Enter the container:

docker exec -ti convert-pheno bash

The command-line executable is available at:

/usr/share/convert-pheno/bin/convert-pheno

The default container user is root, but you can also run as UID=1000 (dockeruser):

docker run --user 1000 -tid --name convert-pheno cnag/convert-pheno:latest

Use make​

If you prefer, use the included makefile.docker:

make -f makefile.docker install
make -f makefile.docker run
make -f makefile.docker enter

Mount Volumes​

Containers are isolated, so mount a host directory when you need to read or write local data:

docker run -tid --volume /media/mrueda/4TBT/data:/data --name convert-pheno-mount cnag/convert-pheno:latest

One convenient pattern is to create an alias on the host:

alias convert-pheno='docker exec -ti convert-pheno-mount /usr/share/convert-pheno/bin/convert-pheno'
convert-pheno -ibff /data/individuals.json -opxf pxf.json --out-dir /data

System Requirements​

  • Supported targets: linux/amd64 and linux/arm64
  • Perl 5.26+ inside the image
  • At least 4 GB RAM
  • At least 1 CPU core
  • At least 16 GB disk space

Optional Athena-OHDSI Database​

If you need --ohdsi-db, download ohdsi.db separately and either place it under share/db/ in a local checkout or mount it into the container and point to it with --path-to-ohdsi-db.

You can either download it manually in a browser from this Google Drive directory:

or download the file from the command line with gdown:

pip install gdown
import gdown

url = "https://drive.google.com/uc?export=download&id=1zQ26Q1qsqTBPDGrtZbhDP-85NhaOrfBP"
output = "./ohdsi.db"
gdown.download(url, output, quiet=False)