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Non-Containerized Installation

Use this path when you want to run convert-pheno directly from CPAN, GitHub, or inside your own Perl environment.

System Dependencies​

On Debian-based distributions, install:

sudo apt-get install cpanminus libbz2-dev zlib1g-dev libperl-dev

Also install the following when your install path pulls the full dependency set from cpanfile or Makefile.PL:

sudo apt-get install libssl-dev

In practice, this matters for repository installs such as cpanm --notest --installdeps . and for dependencies like JSONLD, IO::Socket::SSL, and Net::SSLeay.

Method 1: From CPAN​

Option 1: Install Under ~/perl5​

cpanm --local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)
cpanm --notest Convert::Pheno
convert-pheno --help

To make the local Perl library persistent across shells:

echo 'eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)' >> ~/.bashrc

To update later:

cpanm Convert::Pheno

Method 2: CPAN In A Conda Environment​

This path is useful when you want an isolated environment but still want to run the non-containerized CLI or Perl module.

Step 1: Install Miniconda​

The following example targets x86_64 Linux systems:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Close and reopen the terminal after the installer finishes.

Step 2: Configure Channels​

Set up the channels required by Bioconda:

conda config --add channels bioconda

It is better to install into a fresh environment to avoid dependency conflicts.

Step 3: Create The Environment And Install​

conda create -n myenv
conda activate myenv
conda install -c conda-forge gcc_linux-64 perl perl-app-cpanminus
# conda install -c bioconda perl-mac-systemdirectory   # macOS only
cpanm --notest Convert::Pheno
convert-pheno --help

Replace myenv with your preferred environment name.

To deactivate the environment:

conda deactivate

Method 3: From GitHub​

Clone the repository:

git clone https://github.com/cnag-biomedical-informatics/convert-pheno.git
cd convert-pheno

Update an existing clone:

git pull

Option 1: Install Dependencies Under ~/perl5​

cpanm --local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)
cpanm --notest --installdeps .
bin/convert-pheno --help

If this step fails in Net::SSLeay, IO::Socket::SSL, or JSONLD, make sure libssl-dev is installed and rerun it.

Persist the local Perl library:

echo 'eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)' >> ~/.bashrc

Athena-OHDSI Database​

Some OMOP workflows need 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)

Once downloaded, either:

  1. Move ohdsi.db into share/db/.
  2. Keep it elsewhere and pass --path-to-ohdsi-db.