Command line quickstart

Installing Python Package manually

If Python version 3.6 or newer is 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 Components

Now that the OpenCRAVAT python package is installed, you must install the base OpenCRAVAT modules. Run the following command.

oc module install-base

One of the base components, hg38 gene mapper, requires downloading 2 Gb of data.

Install an Annotator

You can search for annotators to install with the command

oc module  ls -a -t annotator

This also tells you which annotators you have installed.

You can also use regular expressions to filter annotators by their names.

oc module  ls -a cosmic.* -t annotator

To install an annotator use:

oc module  install <annotator name>

For this Quickstart, we install the ClinVar annotator as an example. Run the following command

oc module  install clinvar

Test Run

OpenCRAVAT is now ready to use. With the base components installed, OpenCRAVAT can annotate variants with genes and sequence ontology. We’ve also installed the ClinVar annotator.

If you want, you can test if OpenCRAVAT is working properly using a built-in test input. Create a new directory, and make it the working directory. Make the test input file with

oc new example-input .

which will create example_input in the current working directory. If you want to create the file in another directory, replace “.” with the path to the directory.

Then, run OpenCRAVAT on the test input file with

oc run ./example_input -l hg38

If example_input is not in the current working directory, use the full path to example_input instead of just “example_input”. The run will create many files, all with the prefix “example_input.”.

Once the job is finished, it will create a sqlite database with the results. This sqlite database can be opened in the OpenCRAVAT web viewer with the command

oc gui example_input.sqlite

Instructions for using oc gui and the web viewer are here.