1. Installation

Auto Installation

It's coming, I promise... but it's not too hard to follow the below!

Manual Installation

I recommend creating a separate environment from which you can exclusively control dependencies for Clinker. My preferred method is to use the Anaconda platform, but feel free to use any other method (or none at all) and just skip to step 2.

Create Clinker Environment With Anaconda

Install Anaconda

Follow the install instructions at continuum, but pretty much just:

1. Download Anaconda (you can use wget)
2. Navigate to downloaded file
3. bash Anaconda-latest-Linux-x86_64.sh
4. conda update conda

Activate bioconda

Enter the below in order (!important)

conda config --add channels conda-forge conda config --add channels defaults conda config --add channels r conda config --add channels bioconda

Create Clinker Environment

Now with Anaconda installed, we can simply just create a new environment with Python 2.7 (I know) enabled.

1. conda create --name clinker python=2.7 anaconda

You can always remove this by simply entering

conda remove --name clinker --all

Activate Clinker Environment

1. source activate clinker

All done! Let's start installing the dependencies.

Install Dependencies

Install R, Samtools, STAR

1. conda install -c r r-essentials
2. conda install samtools
3. conda install -c bioconda star=2.5.3a

Install Gviz

Start R and then enter

1. source("https://bioconductor.org/biocLite.R")
2. biocLite("Gviz")

Close R, that's it for dependencies.

Clone latest Clinker

Now we're ready to download the Clinker source!

1. Create a new folder for your Clinker program to reside, navigate there.
2. git clone https://github.com/Oshlack/Clinker.git

You're all done! Ready to work through some examples?