Here is a step by step guide how to install chip-qc on your system. It will get your required python libraries installed and provides a list of R dependencies below.
First, python needs to be installed, if it does not exist yet on the system . Then check, if the package manager pip is present as well.
| Package | version |
|---|---|
| python | > 2.7.5 (but not 3.*) |
Once python and pip are working, you can install the requirements by using:
pip install -r requirements.txt
or if you don't have permissions to install python libraries, you can install it into your own user libary using --user:
pip install -r requirements.txt --user
The last step to complete the installation of chip-qc is the execution of setup.py using the following command. Add --user at the end for the user library:
python setup.py install
❗ To reinstall or upgrade the package, you should run:
python setup.py install --upgrade
The free statistical softer package R is used for calculations and graphics in chip-qc.
R (tested for 3.1.2) RSQLite reshape ggplot2 RColorBrewer
From bioconductor: biocLite("Gviz") biocLite("rtracklayer") biocLite("biomaRt")