If you are familiar with Python and the pip application and your system is already configured (compilers, development libraries available), these two commands should install DREAMTools and its dependencies (in unix or windows terminal):
pip install cython pip install dreamtools
If you do not have dependencies installed yet (e.g., pandas, numpy, scipy), this may take a while depending on your system (typically 10-15 minutes). If you are in a hurry or do not want to compile libraries, see the Anaconda solution here below.
If you are not familiar with Python, or have issues with the previous method (e.g., compilation failure), or do not have root access, we would recommend to use the Anaconda solution.
Anaconda is a free Python distribution. It includes most popular Python packages for science and data analysis and has dedicated channels. One such channel is called `bioconda >https://bioconda.github.io/>`_ and complements the default channel (conda) with a set of packages dedicated to life science.
We have included DREAMTools in bioconda channel. So, once Anaconda is installed, you first need to add the bioconda channel to your environment (and R channel):
conda config --add channels r conda config --add channels bioconda
This should be done only once. Then, install DREAMTools itself:
conda install dreamtools
This command should install DREAMTools in your default conda environment. If you wish to try DREAMTools in another (independent) environment (e.g., a different python version), you would need to create and activate the environment first:
conda create --name test_dreamtools python=3.5 source activate test_dreamtools conda install dreamtools
The previous methods relies on released versions of DREAMTools. If a new feature is only available in the source code, then you will need to get the source code, which is available in the github repository:
git clone firstname.lastname@example.org:dreamtools/dreamtools.git cd dreamtools python setup.py install
Dependencies (e.g. Pandas) will need to be compiled or pre-installed (see above).
We do not provide any DREAMTools package on bioconda for Windows.
However, if you use Anaconda and decide to compile the source yourself under Windows, then you will have to install a compiler that is compatible with Anaconda. In other words, you will have to use the same compiled as the one used by Anaconda.
For Python 2.7, compilation should work easily. You need to know that pre-compiled packages (e.g., Cython) used a specific version of a compiler (http://docs.continuum.io/anaconda/faq#how-did-you-compile-cpython), which is Visual Studio version 2008 and is provided by Microsoft (http://www.microsoft.com/en-us/download/details.aspx?id=44266) for free.
For Python3.4 and 3.5, this is a bit more difficult. You should get Visual C version 2010 (http://stackoverflow.com/questions/29909330/microsoft-visual-c-compiler-for-python-3-4) or for Python 3.5 another Visual C version 2015. This may change with time but this information was found on Anaconda documentation (March 2016). You may found useful information here as well for VS2015: http://www.microsoft.com/en-us/download/details.aspx?id=44266