Clone the repository from Github and put it in your path (or add the direct path to config file)

$ git clone https://github.com/vborjesson/TC_hunter.git
$ export PATH="/home/yourPath/TC_hunter":$PATH
$ source ~/.bashrc

Install required programs and tools using Anaconda

$ conda env create --file TC_hunter/Scripts/TC_hunter.yml
$ source activate TC_hunter

Install every program manually

• Nextflow v.19.01.0
• BWA MEM v.0.7.5a (only if you run TC_hunter_BWA.nf)
• Samtools v.1.9
• R v.3.5.1
• python v.2.7.11
• igv v.2.1.7 (You can choose to run this separately fom the pipeline)