Installation

OMOP CSV Validator is used as a command-line program; using it does not require writing or understanding Perl.

Route	Use it when
CPAN	Perl is already available and you want the smallest installation
Docker or Apptainer	You do not want Perl modules or compiler tools installed on the host
Repository checkout	You are developing or testing the project itself

Install from CPAN

Native dependencies

Some dependencies contain C extensions. CPAN builds these automatically, but a C compiler and development headers must already be installed. Installing under ~/perl5 does not require administrator rights; if the build tools are missing and you cannot install system packages, use the container option below.

Install under ~/perl5

This keeps OMOP CSV Validator and its Perl modules in your home directory and does not modify the system Perl. This route uses cpanm.

If cpanm is not yet available, install it on Debian or Ubuntu:

sudo apt-get install cpanminus

Without sudo, install it into your user-configured Perl environment:

curl -L https://cpanmin.us | perl - App::cpanminus

Create the local Perl library, activate it in the current shell, and install the validator:

cpanm --local-lib=~/perl5 local::lib
eval "$(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)"
cpanm -n OMOP::CSV::Validator
omop-csv-validator --version

Make the local library available in future Bash sessions:

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

Use the standard CPAN client

The standard CPAN client is included with Perl:

cpan OMOP::CSV::Validator
omop-csv-validator --version

If CPAN reports missing build tools on Debian or Ubuntu

Install the standard compiler and Perl development files, then repeat the CPAN command:

sudo apt-get install build-essential libperl-dev

Container alternative

The published image contains release 0.05 and all of its runtime dependencies. It supports Linux amd64 and arm64.

Docker

Pull the versioned image and check the installed command:

docker pull manuelrueda/omop-csv-validator:0.05
docker run --rm manuelrueda/omop-csv-validator:0.05 --version

Mount the current directory as /data when validating local files:

docker run --rm \
  --volume "$PWD:/data" \
  manuelrueda/omop-csv-validator:0.05 \
  --ddl /data/ddl/OMOPCDM_postgresql_5.4_ddl.sql \
  --input /data/PERSON.csv

Both the DDL and CSV must be inside the mounted directory. Report paths should also use /data/... so generated files are written back to the host.

Apptainer

Apptainer can run the same Docker Hub image without installing Perl on the host:

apptainer exec \
  docker://manuelrueda/omop-csv-validator:0.05 \
  omop-csv-validator --version

Validate files from the current directory with an explicit bind mount:

apptainer exec \
  --bind "$PWD:/data" \
  docker://manuelrueda/omop-csv-validator:0.05 \
  omop-csv-validator \
  --ddl /data/ddl/OMOPCDM_postgresql_5.4_ddl.sql \
  --input /data/PERSON.csv

Development installation

Use a repository checkout when changing the code, running the test suite, or reading the development files.

Install the required tools on Debian or Ubuntu:

sudo apt-get install cpanminus build-essential libperl-dev

Clone the repository and install its dependencies:

git clone https://github.com/CNAG-Biomedical-Informatics/omop-csv-validator.git
cd omop-csv-validator
cpanm -n --installdeps .
prove -l t/

The checkout command is available at:

bin/omop-csv-validator --version