deepTools address the challenge of visualizing the large amounts of data that are now routinely generated from sequencing centers in a meaningful way. To do so, deepTools contain useful routines to process the mapped reads data through removal of duplicates and different filtering options to create coverage files in standard bedGraph and bigWig file formats. deepTools allow the creation of normalized coverage files or the comparison between two files (for example, treatment and control). Finally, using such normalized and standardized files, multiple visualizations can be created to identify enrichments with functional annotations of the genome. For a gallery of images that can be produced and a description of the tools see http://f1000.com/posters/browse/summary/1094053

The easiest way to install deepTools is by downloading the source file and using python pip or easy_install tools:

$ pip install deepTools
$ vim [deepTools folder]/config/deepTools.cfg

The deepTools.cfg file contains several variables that need to be adjusted.

Other option is to clone the repository

$ git clone https://github.com/fidelram/deepTools

Then go to the deepTools directory, edit the deepTools.cfg file and then run the install script a:

$ cd deepTools
$ vim config/deepTools.cfg
$ python setup.py install

By default, the script will install python library and executable codes globally, which means you need to be root or administrator of the machine to complete the installation. If you need to provide a nonstandard install prefix, or any other nonstandard options, you can provide many command line options to the install script.

$ python setup.py --help

To install under a specific location use:

$ python setup.py install --prefix <target directory>

deepTools can be easily integrated into Galaxy. All wrappers and dependencies are available in the Galaxy Tool Shed.

At 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:8080 --url http://testtoolshed.g2.bx.psu.edu/ -o bgruening -r c8a0dc481493 --name deeptools --tool-deps --repository-deps --panel-section-name deepTools

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

hg identify http://testtoolshed.g2.bx.psu.edu/repos/bgruening/deeptools

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

• go to the admin page
• select Search and browse tool sheds
• Galaxy test tool shed → Sequence Analysis → deeptools
• install deeptools

For support, questions, or feature requests contact: deeptools@googlegroups.com