Installation — deepTools 3.5.6 documentation (original) (raw)
Remember – deepTools are available for command line usage as well as forintegration 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 conda-forge -c bioconda deeptools
Note that for ARM architecture (e.g. M1 on OSX) you could go via the pip installation (see below), or install via the osx-64 env:
$ CONDA_SUBDIR=osx-64 conda create -c conda-forge -c bioconda -n deeptools deeptools
Command line installation using pip
deepTools can also be installed using pip. You can either install the latest release from pypi:
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 https://github.com/deeptools/deepTools.git $ 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 Galaxy API (recommended)
First generate an API Keyfor 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 https://toolshed.g2.bx.psu.edu/
-o bgruening -r --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 https://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