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


  • Python 2.7 or Python 3.x
  • numpy >= 1.8.0
  • scipy >= 0.17.0
  • py2bit >= 0.1.0
  • pyBigWig >= 0.2.1
  • pysam >= 0.8
  • matplotlib >= 1.4.0

The fastest way to obtain Python 2.7 or Python 3.x together with numpy and scipy is via the Anaconda Scientific Python Distribution. Just download the version that’s suitable for your operating system and follow the directions for its installation. All of the requirements for deepTools can be installed in Anaconda with:

$ conda install -c bioconda deeptools

Command line installation using pip

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 without pip

You are highly recommended to use pip rather than these more complicated steps.

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

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/deepTools2.0

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.