Remember – deepTools are available for command line usage as well as for integration into Galaxy servers !

Command line installation using conda

The recommended way to install deepTools (including its requirements) is via miniconda or anaconda.

$ conda install -c bioconda deeptools

Command line installation using pip

deepTools can also be installed using pip. You can either install the latest release from pypi:

$ pip install deeptools

or a specific version with:

$ pip install deeptools==3.5.3

In case you would like to install an unreleased or development version, deepTools can also be installed from the repository:

$ git clone
$ cd deepTools
$ pip install .

Galaxy installation

deepTools can be easily integrated into a local Galaxy. All wrappers and 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 –> Sequence Analysis –> deeptools

  • install deeptools

deepTools Galaxy.

code @ github.