Installing deepTools

For instructions on using deepTools 2.0 or newer, please go here. This page only applies to deepTools 1.5

WIKI-START > deepTools technical documentation > deepTools installation

Dependencies

The following software is required for proper installation and usage of deepTools:

• Python 2.7
• numpy
• scipy
• pysam (>= 0.7.7)

Installation --------------- * [Installing deepTools within a local _Galaxy instance_](#galaxy) * [Installing deepTools with a _Galaxy instance_ using _docker_](#dockergalaxy) * [Installing deepTools from source (Linux)](#linux) * [Installing deepTools on a Mac](#mac) * [Troubleshooting](#trouble)

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Galaxy Installation

deepTools can be easily integrated into the Galaxy framework. 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: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 revision number from the test tool shed or via the command line with the following command:

hg identify http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools

You can watch the installation status within Galaxy: 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

Using deepTools and Galaxy from a docker Image

At first you need to install docker. Please follow the instruction on https://www.docker.io/gettingstarted/#h_installation

After the successful installation, all what you need to do is:

docker run -d -p 8080:80 bgruening/galaxy-deeptools

I will shortly explain the meaning of all the parameters. For a more detailed describtion please consult the docker manual, it's really worth reading.

Let's start: docker run will run the Image/Container for you. In case you do not have the Container stored locally, docker will download it for you. -p 8080:80 will make the port 80 (inside of the container) available on port 8080 on your host. Inside the container a Apache Webserver is running on port 80 and that port can be bound to a local port on your host computer. With this parameter you can access your Galaxy instance via http://localhost:8080 immediately after executing the command above. bgruening/galaxy-deeptools is the Image/Container name, that directs docker to the correct path in the docker index. -d will start the docker container in daemon mode.

For more information please refer to the project site.

Installation from source (Linux, command line)

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

Requirements: Python 2.7, numpy, scipy installed

Commands:

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

If pip is not already available, install it with:

  $ easy_install --prefix=~ pip

Install deepTools and dependencies with pip:

  $ pip install --user deeptools

Done!

Another option is to clone the repository:

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

Then go to the deepTools directory, edit the deepTools.cfg file with your favorite editor (e.g. vim) and run the install script:

$ 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 non-standard install prefix, or any other non-standard options, you can provide many command line options to the install script.

$ python setup.py --help

For example, to install deepTools 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 might demand a bit of extra work.

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

 $ pip install deeptools

Done!

If you prefer to install the dependencies individually, follow these steps (Python 2.7 must already be installed):

Download the packages and install them using dmg images:

• http://sourceforge.net/projects/numpy/files/NumPy/
• http://sourceforge.net/projects/scipy/files/scipy/

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: see http://www.scipy.org/install.html

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