Installation¶
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/
- R (>= 3.0): https://www.r-project.org/
- R packages including UpSetR, corrplot
Install BEDTools¶
Intervene is using pybedtools, which is Python wrapper for BEDTools. So, BEDTools should be installed before using Intervene It’s recomended to have a latest version, but if you have an older version already install, it should be fine. Please read the instructions at https://github.com/arq5x/bedtools2 to install BEDTools, and make sure it is on your path and you are able to call bedtools from any directory.
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 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 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 requires Python modules individually, you can use the following commands, else you can install Intervene directly.
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 required R packages¶
- Intervene requires two R packages,
UpSetR
https://cran.r-project.org/package=UpSetR - and
corrplot
https://cran.r-project.org/package=corrplot for visualization. To install these open R/RStudio and use the following command.
install.packages(c("UpSetR", "corrplot"))
Install Intervene¶
You can install a stable version of Intervene by using pip
from PyPi or a development version by using git
from GitHub.
Install using pip¶
You can install InterVene either from PyPi using pip or install it from the source. Please make sure you have already installed the above mentioned python libraries required to run InterVene.
Install from PyPi:
pip install intervene
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 install