Metadata-Version: 1.0
Name: deepTools
Version: 1.5.9
Summary: Useful library to deal with mapped reads in sorted BAM format.
Home-page: http://pypi.python.org/pypi/deepTools/
Author: Fidel Ramirez, Friederike Dündar, Björn Grüning, Sarah Diehl
Author-email: deeptools@googlegroups.com
License: LICENSE.txt
Description: ======================================================================
        deepTools
        ======================================================================
        ### 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
        
        ![gallery](https://raw.github.com/fidelram/deepTools/master/examples/collage.png)
        
        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
        
        
        -------------------------------------------------------------------------------------------------------------------
        
        <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.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
        
        <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
        
        ------------------------------------
        [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)
        
Platform: UNKNOWN
