Installing PanTools

There are multiple options for installing PanTools:

1. Install from bioconda (recommended)

2. Install from download

3. Installing PanTools from source (for developers)

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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:

$ curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
$ bash Miniforge3-$(uname)-$(uname -m).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

Now, 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.

$ mamba create -n pantools pantools

Note

If this doesn’t work, you can try to install PanTools using the following way:

$ mamba create -n pantools --strict-channel-priority -c conda-forge -c bioconda pantools=4.3.1

Please make sure to activate the environment before using PanTools:

$ conda activate pantools

Test if PanTools is executable:

$ pantools --help

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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

All dependencies are listed in conda.yaml which can be found on the release page.

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

$ curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
$ bash Miniforge3-$(uname)-$(uname -m).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

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

$ mamba env create -n pantools -f conda.yaml

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-4.3.1.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-4.3.1.jar'" >> ~/.bashrc

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

$ source ~/.bashrc
pantools --help

Download MCScanX

MCScanX is the tool PanTools uses for calculating synteny between genomes or sequences. Since the tools is unavailable in conda, it needs to be downloaded and manually installed from https://github.com/wyp1125/MCScanX. After installation, you can add MCScanX to your path:

$ echo "export PATH=/path/to/MCScanX:$PATH" >> ~/.bashrc
$ source ~/.bashrc