Technical documentation

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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>

### Installation on a MAC

Although the installation of deepTools itself is quite simple, the installation of the required modules SciPy and NumPy demand a bit of extra work.

The easiest way is to install them is together with the Anaconda Scientific Python Distribution. After installation, open a terminal ("Applications" --> "Terminal"): and type:

 $ pip install deeptools

In case the individual installation of the dependencies is prefered follow the next steps:

Requirement: Python 2.7 installed

Download the packages and install them using dmg images:

Then install deepTools via the terminal ("Applications" --> "Terminal"):

 $ cd ~
 $ export PYTHONPATH=$PYTHONPATH:~/lib/python2.7/site-packages
 $ export PATH=$PATH:~/bin:~/.local/bin:~/Library/Python/2.7/bin

If pip is not already available, install with:

 $ easy_install --prefix=~ pip

Install deepTools and dependencies with pip:

 $ pip install --user deeptools

##### Troubleshooting The easy_install command is provided by the python package setuptools. You can download the package from https://pypi.python.org/pypi/setuptools

 $ wget https://bitbucket.org/pypa/setuptools/raw/bootstrap/ez_setup.py -O - | python

or the user-specific way:

 $ wget https://bitbucket.org/pypa/setuptools/raw/bootstrap/ez_setup.py
 $ python ez_setup.py --user

Numpy/Scipy Installation: http://www.scipy.org/install.html

#### Galaxy Installation

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

Installation via Galaxy API (recommended)

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://toolshed.g2.bx.psu.edu/ -o bgruening -r <revision> --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://toolshed.g2.bx.psu.edu/view/bgruening/deeptools

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

Installation via webbrowser

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

remember: for support, questions, or feature requests contact: [email protected]

General information about deepTools usage ---------------------------------------------------------

All tools require the user to specify input files, output file names, optional and mandatory parameters.

Here we point out some parameters that you might find especially useful in your regular usage of deepTools.

Parameters to decrease the run time

numberOfProcessors
region - in case you're testing whether a certain plot works and gives you the output you're hoping for, you can speed things up by focusing on a certain genome region, e.g. chr4 or chr2:100000200000

filtering BAMs while processing

ignoreDuplicates
minMappingQuality

random tips

output format of plots should be indicted by the file ending, e.g. MyPlot.pdf will return a pdf, MyPlot.png a png-file
all tools that produce plots can also output the underlying data - this can be useful in case you don’t like the deepTools visualization as you can then use the data matrices produced by deepTools with your favourite plotting module, e.g. R or Excel