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Non-Containerized Installation

First install the core system dependencies:

sudo apt-get install gcc make cpanminus libperl-dev

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

sudo apt-get install qrencode zbar-tools

We use cpanm to install the CPAN modules. We'll install the dependencies at ~/perl5:

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

To ensure Perl recognizes your local modules every time you start a new terminal, you should type:

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

To update to the newest version:

cpanm ClarID::Tools

Method 2: Download from GitHub​

First, we need to install a few system components:

sudo apt install gcc make git cpanminus libperl-dev

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

sudo apt install qrencode zbar-tools

Use git clone to get the latest (stable) version:

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

If you only need to update to the latest version, do:

git pull

We use cpanm to install the CPAN modules. We'll install the dependencies at ~/perl5:

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

Testing the deployment:

prove

To ensure Perl recognizes your local modules every time you start a new terminal, run:

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

System requirements​

  • OS/ARCH supported: linux/amd64 and linux/arm64.
  • Ideally a Debian-based distribution (Ubuntu or Mint), but any other (e.g., CentOS, OpenSUSE) should do as well (untested).
  • Perl 5 (>= 5.36 core; installed by default in many Linux distributions). Check the version with perl -v
  • 1GB of RAM
  • >= 1 core (ideally i7 or Xeon).
  • At least 5GB HDD.

Platform Compatibility​

This distribution is written in pure Perl and is intended to run on any platform supported by Perl 5. It has been tested on Debian Linux and macOS. It is expected to work on Windows; please report any issues.

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.