Installation
=============
Remember -- deepTools are available for **command line usage** as well as for
**integration into Galaxy servers**!
.. contents::
:local:
Requirements
-------------
* Python 2.7 or Python 3.x
* numpy >= 1.8.0
* scipy >= 0.17.0
* py2bit >= 0.1.0
* pyBigWig >= 0.2.1
* pysam >= 0.8
* matplotlib >= 1.4.0
The fastest way to obtain **Python 2.7 or Python 3.x together with numpy and scipy** is
via the `Anaconda Scientific Python
Distribution `_.
Just download the version that's suitable for your operating system and
follow the directions for its installation. All of the requirements for deepTools can be installed in Anaconda with:
.. code:: bash
$ conda install -c bioconda deeptools
Command line installation using ``pip``
-----------------------------------------
Install deepTools using the following command:
::
$ pip install deeptools
All python requirements should be automatically installed.
If you need to specify a specific path for the installation of the tools, make use of `pip install`'s numerous options:
.. code:: bash
$ pip install --install-option="--prefix=/MyPath/Tools/deepTools2.0" git+https://github.com/deeptools/deepTools.git
Command line installation without ``pip``
-------------------------------------------
You are highly recommended to use `pip` rather than these more complicated steps.
1. Install the requirements listed above in the "requirements" section. This is done automatically by `pip`.
2. Download source code
::
$ git clone https://github.com/deeptools/deepTools.git
or if you want a particular release, choose one from https://github.com/deeptools/deepTools/releases:
::
$ wget https://github.com/deeptools/deepTools/archive/1.5.12.tar.gz
$ tar -xzvf
3. install the source code (if you don't have root permission, you can set
a specific folder using the ``--prefix`` option)
::
$ python setup.py install --prefix /User/Tools/deepTools2.0
Galaxy installation
--------------------
deepTools can be easily integrated into a local `Galaxy `_.
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/ \
--url http://toolshed.g2.bx.psu.edu/ \
-o bgruening -r --name suite_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 with the following
command:
::
$ hg identify http://toolshed.g2.bx.psu.edu/repos/bgruening/suite_deeptools
You can watch the installation status under: 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
Installation with Docker
^^^^^^^^^^^^^^^^^^^^^^^^
The deepTools Galaxy instance is also available as a docker container, for those wishing to use the Galaxy framework but who also prefer a virtualized solution. This container is quite simple to install:
::
$ sudo docker pull quay.io/bgruening/galaxy-deeptools
To start and otherwise modify this container, please see the instructions on `the docker-galaxy-stable github repository `__. Note that you must use `bgruening/galaxy-deeptools` in place of `bgruening/galaxy-stable` in the examples, as the deepTools Galaxy container is built on top of the galaxy-stable container.
.. tip:: For support or questions please make a post on `Biostars `__. For feature requests or bug reports please open an issue `on github `__.