quickstart

Rick Kim edited this page Jan 9, 2019 · 11 revisions

Quickstart

A basic install of OpenCRAVAT consists of three components: python, the open-cravat python package, and a base set of reference data, loaded using OpenCRAVAT's module manager.

Install python

Follow the instructions on python.org to install python version 3.5 or newer. You must included pip, python's package manager in your install.

For Mac OS: We recommend installing Python 3 using the installation file provided at python.org instead of using any other manual way of installing Python 3. After installing Python 3, a new terminal should be opened and used in executing the below commands. Any terminal session which was already open before installing Python 3 will not work properly with open-cravat 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

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. If you are using anaconda, the base command is conda.

If you use Windows and if your Python 3 is installed inside of a system-level folder such as "C:\Program Files", you may have a problem with running open-cravat without the admin privilege. In this case, we recommend installing Python 3 outside of system-level folders and then installing open-cravat.

Install base modules

Now that the OpenCRAVAT python package is installed, you must install the base cravat 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.

Starting the web interface

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.

wcravat

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.

Installing base modules

The initial page of the web interface looks like this.

This page will be used later to submit jobs. For now, click on the store tab in the top left to bring up the module store. It should look like this.

Click the Install base components button in the yellow area. This will start downloading the modules. 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 each module's panel. Leaving the page will not affect the downloads.

Install an annotator

Once the base install is finished, refresh the page and navigate back to the store tab. It should now default to showing available annotators.

We will install the clinvar module, because 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. Wait until the install is finished, then navigate back to the Jobs tab to submit a test job.

Submitting a job

To submit a test job, click on either the CRAVAT format or VCF format buttons in the variants panel at the left, underneath the text box. 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 at the top of the jobs table on the right. The status column should say "Submitted". As the job runs, you can click the Refresh Table button to view the current status of the job.

When a job is finished, launch the web viewer in a new tab by clicking the Launch 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

On the terminal where you started wcravat, press Ctrl-c. On some operating systems, Ctrl-c may be well executed with wcravat. In that case, press Ctrl-break. If your computer does not have a break key, usually there is a key combination that produces the effect of a break key. Examples of alternative key combinations for ctrl-break are: Ctrl+Fn+Esc, Ctrl+Fn+B, Ctrl+Fn+F11, Ctrl+Fn+Shift.

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