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Please note: Users that wish to run the installed Oncotator on the Broad cluster, should follow the instructions here, instead of this page
Both packages are simple tar files that can be expanded using the following commands:
$ tar zxvf oncotator-184.108.40.206.tar.gz $ tar zxvf oncotator_v1_ds_June112014.tar.gz
This will produce two directories called
oncotator_v1_ds_June112014, respectively. Move to the
oncotator-220.127.116.11 directory by doing:
$ cd oncotator-18.104.22.168
See the article on platform requirements for a full list of dependencies. This tutorial will show you how to use the virtual environment script we provide to set everything up automagically, and this tutorial will show you how to install dependencies manually if needed (or preferred).
Once you have installed all the necessary dependencies listed above, simply run the standard Python install script which is included with the Oncotator distribution.
$ python setup.py install
Two binaries (executable program files) named
initializeDatasource respectively will be installed into your Python's
bin/ directory. You can test that they were installed by running e.g.:
$ oncotator -h
to invoke the help / usage instructions. You can also do a test run of Oncotator on the
Patient0.snp.maf.txt file provided with the Oncotator distribution (in the
test/testdata/maflite/ directory) with the following command:
$ oncotator -v --db-dir=~/sandbox/oncotator/oncotator_v1_ds_June112014 test/testdata/maflite/Patient0.snp.maf.txt exampleOutput.tsv hg19
where you provide the location of the datasources using the
--db-dir argument. You may need to adapt the file path for the
Patient0.snp.maf.txt file depending on where you run this command from.
This will produce a new file named
exampleOutput.tsv with the appropriate annotations, built against the
Geraldine Van der Auwera, PhD