Installing on Windows
Sentieon is a command line tool. On windows it runs inside of Cygwin. Cygwin provides a linux like shell allowing you to write scripts in bash to automate your pipeline.
Requesting a license
Open the windows command prompt by seaching for
cmd and selecting
Command Prompt from the selections available.
Enter the following command:
ping -a localhost
The output should look like this:
The name after the text
Pinging is the Fully Qualified Domain Name
of you computer. In this example the FQDN is
lachesis.GoldenHelix.local.To get the number of cores on your
computer run the following command in the same command prompt window.
Include this and your Fully Qualified Domain Name to your account representative and they will be able to issue you a trial license.
Setting up the Cygwin Environment
The first step will be to download the zip file that contains the specially packaged Cygwin version that is designed to run the Sentieon Sentieon is a command line tool. This can be downloaded here:
Once the file has finished downloading, unzip it to a location with plenty of space. It is important to have enough space for the reference sequence as well as the input files that will be sequenced, to begin make sure the install location has at least 50GB of space.
Windows_Sentieon.zip file is unzipped, the unzipped folder
should look like this:
The next step is to set up cygwin to run in the unzipped location.
cygwin64 folder is a file called
Cygwin.bat. This holds the
setting we need to change in order for the cygwin program to function
properly in this unzipped location. Right click on the
file and select edit.
This will open up notepad. Next, edit the value after the
command so that the path matches the path to the
directory. When you are done it should look like this:
Save the file and close notepad. Congrats your cygwin environment is ready to go!
Navigating in Cygwin
Once the cygwin environment is setup you can open the cygwin command
prompt by double clicking on the
Cygwin.bat file. Welcome to cygwin.
If you are not familiar with the linux shell there are a couple commands that you should memorize for navigation:
pwd- Print the working directory. This tells you where in the file system you are inside the shell.
ls- List the contents of the current directory. This will show all of the files in your working directory
cd- Change directories. This command allows you to move your working directory around inside the shell.
Use these command to navigate to the unzipped
folder inside of the cygwin shell. Note that in cygwin you will be
able to find the drives connected to your computer in the
Downloading the Resources and Tools
In the cygwin shell enter the
Secondary-Analysis folder. Inside of
the secondary analysis folder there will be two scripts (
build_pipeline.sh) and the
variant_calling.ini file used to
store the settings used by the build_pipeline.sh script.
download.sh script by executing the following command:
The script will start downloading the reference and cygwin tools. This can take some time as the files are quite large.
Once this completes you can use the example script to call variants on a sample following the directions here Creating a Pipeline.