Pipeline for variant discovery for '225'-resistant strains of P. falciparum 3D7 Project from Jenny Thompson and Alan Cowman, Copied from pipeline used Jan-Feb 2017 for 754 data 225 version started May 2017 by Jocelyn Sietsma Penington

Refer to sh/pipeline255.sh

1. Create a new empty directory to hold code, scripts and output
2. Clone this repository: git clone --recursive https://github.com/WEHI-ResearchComputing/resistant-falciparum. Note the recursive argument to bring in the common tool definitions.
3. Create a toil installation.
   • virtualenv toil-env
   • . toil-env/bin/activate
   • pip install toil toil[cwl] cwltool html5lib drmaa
4. Clone the wehi pipeline add on: git clone https://github.com/WEHI-ResearchComputing/wehi-pipeline.git
5. Edit and run the script resistant-falciparum/src/make-input.py to build the input file.
6. Copy resistant-falciparum/src/cwlwehi.py and edit as appropriate (probably won't need modification).
7. Copy resistant-falciparum/src/runall.sh and edit as appropriate
8. Good luck