This information is specific for using Oncotator at the Broad. This includes running Oncotator on the cluster and configurations used specifically at the Broad.
Please note: if you are working on the Broad servers, you do not need to install or upgrade Oncotator. It will be kept up to date on the Broad cluster. But you may need to tweak your environment settings as described below.
1. Deactivate any Python virtual environment
If you are in an active Python virtual environment, you may need to deactivate it. Just run this simple command:
$ deactivate
If you are not sure whether this applies to you, you probably are not using a virtual environment.
2. Activate appropriate packages
You may need to use the python package and import zlib:
reuse .python-2.7.1-sqlite3-rtrees
reuse .zlib-1.2.6
Hopefully, this step can be eliminated in the future.
3. Activate the preset virtual environment
Add the following to your ~/.my.bashrc:
PATH=/xchip/tcga/Tools/oncotator/onco_env/ubin:$PATH
then run the following from the command line:
source ~/.my.bashrc
This will activate a virtual environment that has Oncotator all the dependencies installed. See the public documentation about running Oncotator in a virtual environment for more information on what this means.
4. Test that you can invoke Oncotator
Try calling Oncotator's help page by running:
oncotator --help
If that works (and there's no reason why it shouldn't) you're all set to use Oncotator!
NOTE:
You may run into trouble if you try to run Oncotator on the cluster with the Broad's pyvcf dotkit. If that happens, use the following command
unuse .pyvcf-0.6.3-python-2.7.1-sqlite3-rtrees