Downloading the required files

The first step is to download the Golden Helix scripts which will allow you to create an example pipeline which you can modify to meet your needs.

These scripts require that you are running either RHEL 6 Linux or Ubuntu 14 Linux or newer.

Proxy Settings

You will need to update the system proxy settings to allow for access to the internet. If you are behind a proxy you will need to set the HTTP_PROXY and HTTPs_PROXY variables.

The template for setting these variables looks like this:

export HTTP_PROXY="http://username:password@host:port"

This might look like the following:

export HTTP_PROXY="http://user:secretpassword@10.254.239.1:3128"
export HTTPS_PROXY="http://user:secretpassword@10.254.239.1:3128"

These lines should be added to the "~/.profile" file or if that doesnt exist, they should be added to the "~/.bashrc" file. After the lines have been added, source the files by running the following command to update these variables in your working environment:

source  ~/.profile

or if you edited ~/.bashrc:

source  ~/.bashrc

This will allow the utilities and scripts that follow to access the internet.

Installing Git

You need to have git installed to download the scripts. It can be installed with the following commands:

RHEL

sudo yum install git -y

Ubuntu

sudo apt-get install git -y

Downloading Scripts

The scripts are stored in git repository. To download the scripts use git to clone the repository.

git clone https://goldenhelix.kilnhg.com/Code/Public/Secondary/Secondary-Analysis.git

This will create a directory call Secondary-Analysis. In this directory there will be a collection of scripts to get you started calling variants with Sentieon.

Downloading Tools and Resources

The next step in the setup is to download the Sentieon and Golden Helix software, as well as the reference sequence that is used to align and call the variants.

To do this execute the following command:

./download.sh

This can take quite a bit of time as the reference sequence and it's accompanying files are over 8 gb. After it completes the reference will have been downloaded to the resources folder, and the Sentieon and VarSeq software will have been placed in the tools folder.

The reference that is downloaded is the 1000 Genomes grch37 Decoy. Other references can be used as long as they have been indexed for use with bwa. Please contact Golden Helix support if you would like help setting up a different reference.

When the downloads have finished, proceed to Licensing to generate a request for a license.