Remember – pyGenomeTracks is available for command line usage as well as for integration into Galaxy servers!


Python dependencies:

  • Python >= 3.6

  • numpy >= 1.16

  • intervaltree >= 2.1.0

  • pyBigWig >= 0.3.16

  • hicmatrix >= 15

  • pysam >= 0.14

  • matplotlib == 3.1.1

  • gffutils >= 0.9

  • pybedtools >= 0.8.1

  • tqdm >= 4.20

External dependencies:

  • BEDTools

Command line installation using conda

We encourage users to use conda installation to install pygenometracks. All of the requirements for pyGenomeTracks can be installed via Anaconda with:

$ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks python=3.7

To get a specific version, one can specify it. For example:

$ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks=3.5 python=3.7

Command line installation using pip

Install pyGenomeTracks using the following command:

$ pip install pyGenomeTracks

All python requirements should be automatically installed.

Since version 3.5, pyGenomeTracks require BEDTools, do not forget to install it or load it into your environment.

If you need to specify a specific path for the installation of the tools, make use of pip install’s numerous options:

$ pip install --install-option="--prefix=/MyPath/Tools/pyGenomeTracks" git+

Command line installation without pip

You are highly recommended to use conda install rather than the following complicated steps.

  1. Install the requirements listed above in the “requirements” section. This is done automatically by pip (except BEDTools).

2. Download source code

$ git clone

or if you want a particular release, choose one from

$ wget
$ tar -xzvf

3. install the source code (if you don’t have root permission, you can set a specific folder using the --prefix option)

$ python install --prefix /User/Tools/pyGenomeTracks3.1

Galaxy installation

pyGenomeTracks can be easily integrated into a local Galaxy. The wrapper and its dependencies are available in the Galaxy Tool Shed.

Installation via web browser

  • go to the admin page

  • select Search and browse tool sheds

  • Galaxy tool shed –> Visualization –> pygenometracks

  • install pygenometracks