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Non-Containerized Installation

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

System Dependencies​

On Debian-based distributions, install the core build dependencies:

sudo apt-get install gcc make cpanminus libperl-dev

Install git if you plan to install from GitHub or create a developer checkout:

sudo apt-get install git

If you plan to use clarid-tools qrcode, also install the QR helper tools:

sudo apt-get install qrencode zbar-tools

Install Under ~/perl5​

Install ClarID-Tools and its dependencies in a local Perl library:

cpanm --local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)
cpanm --notest ClarID::Tools
clarid-tools --help

To make the local Perl library persistent across shells:

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

To update later:

cpanm ClarID::Tools

Method 2: From GitHub​

To install the latest GitHub version without cloning the repository, use cpanm directly:

cpanm --notest https://github.com/CNAG-Biomedical-Informatics/clarid-tools.git
clarid-tools --help

Developer Checkout​

Use a full clone only when you want to inspect the source, run tests, or edit the code locally:

git clone https://github.com/CNAG-Biomedical-Informatics/clarid-tools.git
cd clarid-tools

Update an existing clone:

git pull

Install dependencies under ~/perl5:

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

Run the test suite:

prove -lr t

Persist the local Perl library:

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

Platform Compatibility​

  • Perl 5.36 or newer is required. Check the installed version with perl -v.
  • ClarID-Tools is tested on Debian-based Linux distributions and macOS.
  • Other Unix-like systems may work but are not currently tested.
  • Windows support is not currently tested.

The CLI is implemented in Perl, but dependencies such as YAML::XS and Text::CSV_XS include compiled extensions. A compiler and Perl development headers may therefore be required during installation. ClarID-Tools has no special hardware requirements beyond the resources needed for the input data.

Common errors: Symptoms and treatment​

  • clarid-tools qrcode fails with qrencode not found in PATH

    Install qrencode with your system package manager.

  • clarid-tools qrcode fails with zbarimg not found in PATH

    Install zbar-tools with your system package manager.

  • A new terminal cannot find locally installed Perl modules

    Ensure you loaded local::lib, for example by adding:

    eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)

    to your shell startup file.