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 installing dependencies.

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)

1. conda config --add channels conda-forge
2. conda config --add channels defaults
3. conda config --add channels r
4. 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 bpipe

This is an easy one to start off with! Head over to https://github.com/ssadedin/bpipe and download version 0.9.9.7 of bpipe (http://download.bpipe.org/versions/bpipe-0.9.9.7.tar.gz).

You can follow the instructions below, but all you really need to do is extract it somewhere and add the bin folder to your path.

Simon has created a lot of documentation on bpipe http://docs.bpipe.org, please please please check it out... It's cool!

Install R, Samtools, STAR

1. conda install -c r r-essentials
2. conda install samtools // NOTE: requires Samtools v1.11 or higher
3. conda install -c bioconda star=2.5.3a

Install Gviz & Biomart

Start R and then enter

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

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

Test installation

To test whether everything is working as it should just run the below steps:

1. In the location where you cloned Clinker above, export CLINKERDIR=$PWD
2. Navigate to $CLINKERDIR/test
3. then ./test-installation.sh
4. after the pipeline finishes a new plot should appear in $CLINKERDIR/test/results/plots/test/BCR_ABL1.pdf

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

Run Clinker on a bigger scale

Have many researchers who want to use Clinker, but only want to use a single installation? Try the following.

1. Create a new folder, globally accessible by those who you wish to use Clinker.
2. Navigate to this folder and clone a copy of Clinker
   • git clone https://github.com/Oshlack/Clinker.git
3. Most institutions have a method of managing software on their servers (e.g. Modules), whatever method you choose, ensure that all the Clinker dependencies are loaded and the clinker directory is added as an environment variable called $CLINKERDIR (i.e. export CLINKERDIR="/path/to/clinkerdir")
4. Whenever somebody wants to run clinker, they can do so with the usual snippet, but with the following bolded change:

bpipe -p out="/path/to/clinker/output" -p caller="/path/to/jaffa_results.csv" -p col="3,4,5,6" -p del="c" -p genome="19" -p print="true" -p fusions="BCR:ABL1" -p pdf_width="9" -p pdf_height="16" -p sizing="1,3,1,2,4,2" -p competitive="true" $CLINKERDIR/workflow/clinker.pipe /path/to/*.fastq.gz

NOTE: There are many ways to manage a server, this may not be the best method for you. Let us know if you come across another solution and we will add it to the wiki.

WARNING: make sure you edit threads, genome_mem and align_mem to reflect the constraints of your system...