Quickstart

OpenCRAVAT consists of three components: python, the open-cravat python package, and a base set of reference data. For advanced users, command line instructions are available in the Command line quickstart.

Installing with Windows or Mac OS Installer

Windows users: Windows installer

Windows Defender may indicate that it prevented an unknown application from running. If so, click the ‘More’ link on the message and then select ‘Run Anyway’. An “OpenCRAVAT” icon will be created on the Desktop and the Start Menu. Continue this Quickstart from “Install base modules”.

Mac OS users: Mac OS installer

Right-click the downloaded file and select “Open”. Your Mac may ask you to confirm stating that the file was not downloaded from the App Store. Click “Open” button. Just double-clicking the installer may not enable this “Open” option. Continue this Quickstart from “Install base modules”.

Installing Python Package manually

Alternatively, if Python version 3.6 or newer is installed, the OpenCRAVAT Python package can be installed using pip following the instructions below.

Install python

Follow the instructions on python.org to install Python version 3.6 or newer. Pip, python’s package manager, must be included in the installation.

For Mac OS: We recommend installing Python 3 using the installation file provided at python.org. After installing Python 3, a new terminal must be opened to execute the following commands.

For Ubuntu: pip3 provided by apt does not install executables properly. We recommend the following steps before proceeding. sudo apt remove python-pip if pip3 has already been installed with apt. Then wget https://bootstrap.pypa.io/get-pip.py and sudo python3 get-pip.py.

Install open-cravat package

With Python 3.6 or newer installed, run the following command to install the OpenCRAVAT pip package.

pip install open-cravat

Depending on your python configuration, the base command for pip may be be pip3 instead of pip. sudo should be avoided in installing OpenCRAVAT.

If you use Windows and your Python 3 is installed inside of a system-level folder such as “C::raw-latex:`Program `Files”, you may have a problem with running OpenCRAVAT without admin privilege. In this case, we recommend installing Python 3 outside of system-level folders and then installing OpenCRAVAT.

Install base modules

Now that the OpenCRAVAT python package is installed, you must install the base modules. This can be done either through OpenCRAVAT’s web interface, or though the command line interface. This quickstart will continue with instructions using the web interface. Command line instructions are available in the command line quickstart page <quickstart-command-line>.

The web interface is started by running a local web server, then connecting it using a browser. Both these actions can be taken by running the following command in any command shell.

oc gui

This will start a python server in the shell it was run in. It will also open your default web browser to the main page of the web interface. Closing the command line shell will shutdown the server.

The initial page of the web interface looks like this.

Click the Install system modules button to download the required system files. One of the modules, UCSC hg38 Gene Mapper, requires approximately 2 Gb of reference data, and may not download quickly. Download progress will appear in the bottom of the screen. Leaving the page will not affect the downloads.

Install an annotator

Once the base install is finished, navigate to the store tab. It should now show available annotators.

We will install the ClinVar module, as it is relatively small. Clicking on the ClinVar panel will open up a detail panel for that module.

The “Install” button on the top right will install ClinVar. After the installation is finished, navigate back to the Jobs tab to submit a test job.

Submitting a job

To submit a test job, click on either the VCF or tsv buttons underneath the text box in the Variants panel. This will load in a few example variants. Next, click the Annotate button at the bottom to submit the job.

After submission, a new row should appear in the jobs table on the right. The status column should say “Submitted”. As the job runs, the status column will update to reflect the job status.

When a job is finished, launch the web viewer in a new tab by clicking the Open Result Viewer button. This will open up the results viewer in a new tab. Instructions for using the results viewer are available here

Stopping the web interface

In the terminal that opened with OpenCRAVAT, press Cancel and then Quit.

Multiuser support

OpenCRAVAT’s web interface can have multiple user accounts by installing open-cravat-multiuser package (from OpenCRAVAT 1.6.0). See this page for the details of using multiple user accounts with OpenCRAVAT.