This workflow calls variants in a sequence sample by aligning it to a reference genome, identifying variants and annotating them. It reimplements a publication by Koboldt et al. 2013.
A detailed description can be found on the Cuneiform website. This cookbook installs all necessary tools, downloads all necessary data, sets up Cuneiform, and places the workflow in a predetermined location. The cookbook can be run on any system in a virtual machine. For running the cookbook natively, an Ubuntu 14.04 or higher is required.
Below you find installation instructions for, both, the native and the virtual machine setup.
Install the following packages:
If you want to set up a VM to test Cuneiform these additional packages are required:
Under Ubuntu you can install the ChefDK by entering on the command line
sudo dpkg -i chefdk_*.deb
Building a VM with kitchen
This section describes how to set up the workflow environment in a Virtual Machine (VM). To do this, it does not matter whether you are running Linux, Mac OS, or Windows. However, if you are running an Ubuntu and want to set up the workflow locally (without creating a VM), see Section Building locally.
To build a VM from this cookbook for the first time, change your git base directory and enter the following:
git clone https://github.com/joergen7/variant-call.git cd variant-call kitchen converge
You can log into the newly built VM by entering
You can drop the VM by entering
This section describes how to set up this workflow locally without the indirection of a VM. If you want to try out this workflow in a VM first see Section Building a VM with kitchen.
To install this cookbook locally, create a directory "cookbooks", clone the cookbook into it and run the chef client:
mkdir cookbooks cd cookbooks git clone https://github.com/joergen7/variant-call.git cd variant-call berks vendor .. cd ../.. sudo chef-client -z -r "variant-call::default"
Running the Workflow
If you installed the workflow on a VM log into the machine by typing
Execute the workflow script by entering
cuneiform -d /opt/data /opt/wf/variant-call.cf