In the beginning

There are many different ways to install HapLink. Note that some of these install methods are platform-specific.

• In the beginning
• • Bioconda
  • Container install
  • Julia dependent-install

Bioconda

We understand: every bioinformatian is addicted to miniconda. 🐍 And we're not here to judge. 👩‍⚖️ It's easy and portable and is bundled on most HPCs. If you already have conda (or mamba), then this route is probably for you.

Install HapLink inside a conda environment

We'll make a new environment with the totally original name "haplink," to house the new haplink install and add it directly.

conda create -n haplink -c bioconda -c conda-forge haplink -y

Activate the environment

Now that we've made the environment, let's use it!

conda activate haplink

Test for errors

Next, cross your fingers 🤞 and run the following command:

haplink --help

The most common error is

The following package could not be installed
└─ haplink   does not exist (perhaps a typo or a missing channel).

If this happens,

1. Check your spelling in the install command
2. Check that you are using an x86-64 version of conda on Linux

Another common error is

bash: haplink: command not found
bash: /bin/julia: No such file or directory

If this happens, check that CONDA_PREFIX is set correctly by running echo "$CONDA_PREFIX", and/or rerun conda activate haplink.

If there are no error messages, you're done. You can reuse your haplink environment for the next tutorial.

Container install

One option for installing HapLink is don't install HapLink. Or rather, pull a container that already has HapLink installed, and process files inside of it. HapLink provides a Docker container that has been tested on Apptainer. You should be able to use nearly any container software to run HapLink, but we recommend Apptainer, due to its ubiquity on HPCs, simple file permissions, and increased security.

Download the container

With Apptainer installed, run

apptainer pull docker://ghcr.io/ksumngs/haplink.jl

Run the container as a one-off

You can check to see if the container downloaded correctly by using the apptainer exec command.

apptainer exec haplink.jl_latest.sif haplink --version

Enter the container to run multiple commands

For more complex commands, it is often better to enter the container's shell environment and execute commands within the container. Apptainer will include all files in your working directory as part of the container when doing this.

$ apptainer shell haplink.jl_latest.sif
Apptainer> haplink --version

Julia dependent-install

HapLink is unashamedly a Julia program. If you already have Julia installed, then you can leverage that existing Julia install to install HapLink.

Check your Julia version

HapLink requires Julia v1.6 or later to run. No exceptions, Kemosabe. Run a check now to see if you have a high enough version.

julia --version

Add HapLink to a temporary environment and install

Using the magic of Julia's environments, we can do a "temp install" of the HapLink package to a temporary directory environment. Because this is a fresh install, though, it will trigger an installation of the application to a brand-new isolated environment.

julia \
  --startup-file=no \
  --history-file=no \
  --quiet \
  -e 'using Pkg; Pkg.activate(;temp=true); Pkg.add(HapLink)'

Add HapLink to PATH

Comonicon will install HapLink, but chances are it won't be accessible yet. We need to add HapLink to the PATH, first.

Bash

echo 'export PATH=$HOME/.julia/bin:$PATH' >> $HOME/.bashrc
. ~/.bashrc

Zsh

echo 'export PATH=$HOME/.julia/bin:$PATH' >> $HOME/.zshrc
. ~/.zshrc

Testing

Now, run the haplink command.

haplink --help

Wait, the test failed!

Odds are good that you already had an install of HapLink somewhere in your Julia depot. If that happens, then you'll have to trigger the install manually. Just run

julia \
  --startup-file=no \
  --history-file=no \
  --quiet \
  -e 'using Pkg; Pkg.activate(;temp=true); Pkg.add(HapLink); using HapLink; HapLink.comonicon_install()'

then return to the Add HapLink to PATH step.

Success! We now have a working installation of HapLink. You are now ready to move on to the next tutorial.