Installation¶

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

Command line installation using conda
Command line installation using pip from pypi
Command line installation using pip from source
Galaxy installation

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+https://github.com/deeptools/deepTools.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 https://github.com/deeptools/deepTools.git

or if you want a particular release, choose one from https://github.com/deeptools/deepTools/releases:

$ wget https://github.com/deeptools/deepTools/archive/1.5.12.tar.gz
$ 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 Galaxy API (recommended)¶

First generate an API Key for your admin user and run the the installation script:

$ python ./scripts/api/install_tool_shed_repositories.py \
        --api YOUR_API_KEY -l http://localhost/ \
        --url http://toolshed.g2.bx.psu.edu/ \
        -o bgruening -r <revision> --name suite_deeptools \
        --tool-deps --repository-deps --panel-section-name deepTools

The -r argument specifies the version of deepTools. You can get the latest revision number from the test tool shed or with the following command:

$ hg identify http://toolshed.g2.bx.psu.edu/repos/bgruening/suite_deeptools

You can watch the installation status under: Top Panel –> Admin –> Manage installed tool shed repositories

Installation via web browser ¶

go to the admin page
select Search and browse tool sheds
Galaxy tool shed –> Sequence Analysis –> deeptools
install deeptools

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 quay.io/bgruening/galaxy-deeptools

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.

Tip

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.

Installation¶

Command line installation using conda¶

Command line installation using pip from pypi¶

Command line installation using pip from source¶

Galaxy installation¶