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.
This software package is written in the programming language Python, the statistical functional language R and the anayslysis package WiggleTools. Extra extensions are required for processing in addition to the basic installion of both packages. Instruction on how to install chip-qc and the required extensions are listed 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 statistical software package R is used for calculations and graphics in chip-qc. To start with, R and the package manager Bioconductor needs to be installed, if it does not exist on your system.
| Package | version |
|---|---|
| R | 3.1.2 |
Once R and Bioconductor are working on your system, you can install the requirements by using the commands below, following the instruction on you screen:
R
install.packages(c("RSQLite","reshape","ggplot2","RColorBrewer"))
The Bioconductor packages can be installed using the commands below:
R
source("https://bioconductor.org/biocLite.R")
biocLite("Gviz")
biocLite("rtracklayer")
biocLite("biomaRt")
After installing the requirements, the last step to complete the chip-qc installation is the execution of setup.py. This can be done by using the command below - adding --user at the end as required for the user library:
python setup.py install
❗ To reinstall or upgrade the package, you need to run install again:
python setup.py install