Installing PanTools

There are multiple options for installing PanTools:

Install from bioconda (recommended)
Install from download
Installing PanTools from source (for developers)

Install from bioconda

The easiest way to install PanTools is through bioconda. Bioconda is a channel for the conda package manager specializing in bioinformatics software.

For users that don’t have conda installed, we recommend to install conda first:

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

# Follow the instructions on the screen
# Restart your terminal

$ conda config --set auto_activate_base false
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
$ conda config --remove channels defaults
$ conda config --set channel_priority strict

# Restart your terminal

Next, we recommend to install mamba into the conda base environment to enable much faster dependency solving:

$ conda install -n base mamba

Finally, we can install PanTools. We recommend to install PanTools into a separate environment. Please make sure you install the most recent versions of the tools. NB: not all dependencies are available for macOS, therefore please use the correct line from this code block depending on your operating system:

$ mamba create -n pantools pantools bcftools busco  # Linux
$ mamba create -n pantools pantools  # macOS

Please make sure to activate the environment before using PanTools:

$ conda activate pantools

Test if PanTools is executable:

$ pantools --help

Install from download

The second option is to download PanTools from our git page. For this, you will need to install all dependencies separately. We provide YAML files for a conda environment that has all dependencies.

Install dependencies using conda

Please choose the conda_linux.yml or conda_macos.yml file depending on your operating system. These files be found on the release page. The difference between the two files comes from some dependencies conflicting on macOS but not on Linux. Only on Linux a full installation of PanTools is possible. On macOS, some functionalities will not be available.

For users that don’t have conda installed, we recommend to install conda first:

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

# Follow the instructions on the screen
# Restart your terminal

$ conda config --set auto_activate_base false
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
$ conda config --remove channels defaults
$ conda config --set channel_priority strict

# Restart your terminal

Next, we recommend to install mamba into the conda base environment to enable much faster dependency solving:

$ conda install mamba -n base -c conda-forge

Finally, we can install all dependencies into a separate environment:

$ mamba env create -n pantools -f conda_linux.yml #for Linux
$ mamba env create -n pantools -f conda_macos.yml #for macOS

Please make sure to activate the environment before using PanTools:

$ conda activate pantools

Download PanTools

Download the latest release from https://git.wur.nl/bioinformatics/pantools/-/releases. The file to download is named pantools-4.2.1.jar.

Set PanTools alias

To avoid typing long command line arguments every time, we suggest setting an alias to your profile. Set an alias in your ~/.bashrc using the following command. Always include the full path to PanTools .jar file.

Run the following to add the alias to your ~/.bashrc:

$ echo "alias pantools='java -Xms20g -Xmx50g -jar /path/to/pantools-4.2.1.jar'" >> ~/.bashrc

Source your ~/.bashrc and test if the alias works:

$ source ~/.bashrc
pantools --help