Installation¶
Quick installation¶
Install uisng bioconda¶
conda install -c bioconda intervene
This will install all the dependencies and you are ready to use Intervene. Make sure you have R installed.
Install using pip¶
You can install Intervene from PyPi using pip.
Prerequisites¶
Intervene requires the following Python modules and R packages:
- Python (=> 2.7 ): https://www.python.org/
- BEDTools (Latest version): https://github.com/arq5x/bedtools2
- pybedtools (>= 0.7.9): https://daler.github.io/pybedtools/
- Pandas (>= 0.16.0): http://pandas.pydata.org/
- Seaborn (>= 0.7.1): http://seaborn.pydata.org/
- R (>= 3.0): https://www.r-project.org/
- R packages including UpSetR, corrplot
Install BEDTools¶
Intervene is using pybedtools, which is a Python wrapper for the BEDTools. BEDTools should be installed before using Intervene. It is recomended to have the latest version of the tool. Please read the installation instructions at https://github.com/arq5x/bedtools2 to install BEDTools, and make sure it is accessible through your PATH variable.
Install required Python modules¶
Intervene takes care of the installation of all the required Python modules. If you already have a working installation of Python, the easiest way to install the required Python modules is by installing Intervene using pip
. If you're setting up Python for the first time, we recommend to install it using the Anaconda Python distribution http://continuum.io/downloads. These come with several helpful scientific and data processing libraries. These are available for platforms including Windows, Mac OSX and Linux.
If you want to install the required Python modules manually, you can use the following commands.
Install pybedtools
Install it from PyPi
pip install pybedtools
or using conda
conda install -c bioconda pybedtools
Read more details about ''pybedtools'' installation: https://daler.github.io/pybedtools/main.html
Install Pandas
Install it from PyPi
pip install pandas
Or install with conda
conda install pandas
Install Intervene from source¶
You can install a development version by using git
from our bitbucket repository at https://bitbucket.org/CBGR/intervene or Github.
Install development version from Bitbucket¶
If you have git installed, use this:
git clone https://bitbucket.org/CBGR/intervene.git
cd intervene
python setup.py sdist install
Install development version from GitHub¶
If you have git installed, use this:
git clone https://github.com/asntech/intervene.git
cd intervene
python setup.py sdist install