Chef cookbook which sets up many common bioinformatics tools.
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
This section describes how to set up a bioinformatics worker 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/chef-bioinf-worker.git
After cloning the git repository, download the GATK binaries and place them in the files folder so that your cookbook folder contains a file 'files/GenomeAnalysisTK-3.5.tar.bz2'. Now enter the cookbook folder and converge the VM.
cd chef-bioinf-worker
kitchen converge
You can log into the newly built VM by entering
kitchen login
You can drop the VM by entering
kitchen destroy
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/chef-bioinf-worker.git
After cloning the git repository, download the GATK binaries and place them in the files folder so that your cookbook folder contains a file 'files/GenomeAnalysisTK-3.5.tar.bz2'. Now enter the cookbook folder and converge the VM.
cd ..
sudo chef-client -z -r "chef-bioinf-worker::default"
- Jörgen Brandt (@joergen7) [email protected]