def run_oncotator(job, vcf_id, oncotator_db):
job.fileStore.logToMaster('<STR_LIT>')<EOL>inputs = {'<STR_LIT>': vcf_id,<EOL>'<STR_LIT>': oncotator_db}<EOL>work_dir = job.fileStore.getLocalTempDir()<EOL>for name, file_store_id in inputs.iteritems():<EOL><INDENT>inputs[name] = job.fileStore.readGlobalFile(file_store_id, os.path.join(work_dir, name))<EOL><DEDENT>if tarfile.is_tarfile(inputs['<STR_LIT>']):<EOL><INDENT>tar = tarfile.open(inputs['<STR_LIT>'])<EOL>tar.extractall(path=work_dir)<EOL>inputs['<STR_LIT>'] = tar.getmembers()[<NUM_LIT:0>].name<EOL>tar.close()<EOL><DEDENT>command = ['<STR_LIT>', '<STR_LIT>',<EOL>'<STR_LIT>', '<STR_LIT>',<EOL>'<STR_LIT>', inputs['<STR_LIT>'],<EOL>'<STR_LIT>',<EOL>'<STR_LIT>',<EOL>'<STR_LIT>']  <EOL>docker_parameters = ['<STR_LIT>', '<STR_LIT>', '<STR_LIT:none>',<EOL>'<STR_LIT>', '<STR_LIT>'.format(job.memory)]<EOL>dockerCall(job=job, workDir=work_dir,<EOL>parameters=command,<EOL>tool='<STR_LIT>',<EOL>dockerParameters=docker_parameters)<EOL>return job.fileStore.writeGlobalFile(os.path.join(work_dir, '<STR_LIT>'))<EOL>
Uses Oncotator to add cancer relevant variant annotations to a VCF file. Oncotator can accept
other genome builds, but the output VCF is based on hg19.

:param JobFunctionWrappingJob job: passed automatically by Toil
:param str vcf_id: FileStoreID for VCF file
:param str oncotator_db: FileStoreID for Oncotator database
:return: Annotated VCF FileStoreID
:rtype: str