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

Command line installation using conda

DeepTools (including the requirements) can be installed with conda:

$ conda install -c bioconda deeptools

Command line installation using pip from pypi

Install deepTools using the following command:

$ pip install deeptools

All python requirements should be automatically installed.

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/deepTools2.0" git+

Command line installation using pip from source

You are highly recommended to use the ‘pypi installation’ rather than these more complicated steps.

1. Download source code

$ git clone

or if you want a particular release, choose one from

$ wget
$ tar -xzvf

3. install the source code

$ python -m build
$ pip install dist/*whl

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

Installation with Docker

The deepTools Galaxy instance is also available as a docker container, for those wishing to use the Galaxy framework but who also prefer a virtualized solution. This container is quite simple to install:

$ sudo docker pull

To start and otherwise modify this container, please see the instructions on the docker-galaxy-stable github repository. Note that you must use bgruening/galaxy-deeptools in place of bgruening/galaxy-stable in the examples, as the deepTools Galaxy container is built on top of the galaxy-stable container.


For support or questions please make a post on Biostars. For feature requests or bug reports please open an issue on github.

deepTools Galaxy. code @ github.