deepTools 2.2.2

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deepTools
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### user-friendly tools for the normalization and visualization of deep-sequencing data


deepTools addresses the challenge of handling the large amounts of data
that are now routinely generated from DNA sequencing centers. To do so, deepTools contains useful modules to process the mapped reads data to create coverage files in standard bedGraph and bigWig file formats. By doing so, deepTools allows 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, see
http://f1000.com/posters/browse/summary/1094053

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


Our [wiki page](https://github.com/fidelram/deepTools/wiki) contains more information on **why we built deepTools**, details on the **individual tool scopes and usages** and an introduction to our deepTools Galaxy web server. It also contains an [FAQ section](FAQ) that we update regularly. For more specific troubleshooting, feedback, and tool suggestions, contact us via deeptools@googlegroups.com


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<a name="installation"/></a>
Installation
---------------

deepTools are available for:

* command line usage
* integration into Galaxy servers

Details on the installation routines can be found here.

[Installation from source](#linux)

[Installation on a Mac](#mac)

[Troubleshooting](#trouble)

[Galaxy installation](#galaxy)


<a name="linux"/></a>
### 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 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 and then run the install script a:

$ cd deepTools
$ vim deeptools/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>

<a name="mac"></a>
### 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 to install them ois together with the
[Anaconda Scientific Python Distribution][]. After installation, open
a terminal ("Applications" --> "Terminal"): and type:

$ pip install deeptools

If individual installation of the dependencies is preferred, follow
those steps:

Requirement: Python 2.7 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


<a name="trouble"/></a>
##### Troubleshooting
The easy_install command is provided by the python package setuptools.
You can download the package from https://pypi-hypernode.com/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

<a name="galaxy"/></a>
#### Galaxy Installation

deepTools can be easily integrated into [Galaxy](http://galaxyproject.org). All wrappers and dependencies are
available in the [Galaxy Tool Shed](http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools).


##### Installation via Galaxy API (recommended)

At first generate an [API Key](http://wiki.galaxyproject.org/Admin/API#Generate_the_Admin_Account_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](http://localhost:8080/admin)
- select *Search and browse tool sheds*
- Galaxy tool shed → Sequence Analysis → deeptools
- install deeptools

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

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[BAM]: https://docs.google.com/document/d/1Iv9QnuRYWCtV_UCi4xoXxEfmSZYQNyYJPNsFHnvv9C0/edit?usp=sharing "binary version of a SAM file; contains all information about aligned reads"
[SAM]: https://docs.google.com/document/d/1Iv9QnuRYWCtV_UCi4xoXxEfmSZYQNyYJPNsFHnvv9C0/edit?usp=sharing "text file containing all information about aligned reads"
[bigWig]: https://docs.google.com/document/d/1Iv9QnuRYWCtV_UCi4xoXxEfmSZYQNyYJPNsFHnvv9C0/edit?usp=sharing "binary version of a bedGraph file; contains genomic intervals and corresponding scores, e.g. average read numbers per 50 bp"
[bedGraph]: https://docs.google.com/document/d/1Iv9QnuRYWCtV_UCi4xoXxEfmSZYQNyYJPNsFHnvv9C0/edit?usp=sharing "text file that contains genomic intervals and corresponding scores, e.g. average read numbers per 50 bp"
[FASTQ]: https://docs.google.com/document/d/1Iv9QnuRYWCtV_UCi4xoXxEfmSZYQNyYJPNsFHnvv9C0/edit?usp=sharing "text file of raw reads (almost straight out of the sequencer)"

[bamCorrelate]: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamCorrelate
[bamFingerprint]: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint
[computeGCBias]: https://github.com/fidelram/deepTools/wiki/QC#wiki-computeGCbias
[bamCoverage]: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCoverage
[bamCompare]: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare
[computeMatrix]: https://github.com/fidelram/deepTools/wiki/Visualizations
[heatmapper]: https://github.com/fidelram/deepTools/wiki/Visualizations
[profiler]: https://github.com/fidelram/deepTools/wiki/Visualizations

[Benjamini and Speed]: http://nar.oxfordjournals.org/content/40/10/e72 "Nucleic Acids Research (2012)"
[Diaz et al.]: http://www.degruyter.com/view/j/sagmb.2012.11.issue-3/1544-6115.1750/1544-6115.1750.xml "Stat. Appl. Gen. Mol. Biol. (2012)"
[Anaconda Scientific Python Distribution]: https://store.continuum.io/cshop/anaconda/

This tool suite is developed by the [Bioinformatics Facility](http://www1.ie-freiburg.mpg.de/bioinformaticsfac) at the [Max Planck Institute for Immunobiology and Epigenetics, Freiburg](http://www1.ie-freiburg.mpg.de/).

[Wiki Start Page](https://github.com/fidelram/deepTools/wiki) | [deepTools Galaxy](http://deeptools.ie-freiburg.mpg.de) | [FAQ](https://github.com/fidelram/deepTools/wiki/FAQ)