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(howto) Use Oncotator on the Broad servers

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
edited June 2014 in Oncotator documentation

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:


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!


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
Post edited by LeeTL1220 on


  • dmccabedmccabe BostonMember, Broadie

    After following the instructions above I'm getting the below error. It's strange because I could've sworn this worked a few months ago.

    oncotator --help
    Traceback (most recent call last):
      File "/xchip/tcga/Tools/oncotator/onco_env/ubin/oncotator", line 9, in <module>
        load_entry_point('Oncotator==', 'console_scripts', 'oncotator')()
      File "/xchip/tcga/Tools/oncotator/onco_env_2.7.1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 542, in load_entry_point
        return get_distribution(dist).load_entry_point(group, name)
      File "/xchip/tcga/Tools/oncotator/onco_env_2.7.1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2569, in load_entry_point
        return ep.load()
      File "/xchip/tcga/Tools/oncotator/onco_env_2.7.1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2229, in load
        return self.resolve()
      File "/xchip/tcga/Tools/oncotator/onco_env_2.7.1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2235, in resolve
        module = __import__(self.module_name, fromlist=['__name__'], level=0)
      File "build/bdist.linux-x86_64/egg/oncotator/Oncotator.py", line 52, in <module>
      File "build/bdist.linux-x86_64/egg/oncotator/utils/RunSpecificationFactory.py", line 2, in <module>
      File "build/bdist.linux-x86_64/egg/oncotator/DatasourceFactory.py", line 72, in <module>
      File "build/bdist.linux-x86_64/egg/oncotator/datasources/BigWigDatasource.py", line 1, in <module>
      File "/xchip/tcga/Tools/oncotator/onco_env_2.7.1/lib/python2.7/site-packages/numpy/__init__.py", line 180, in <module>
        from . import add_newdocs
      File "/xchip/tcga/Tools/oncotator/onco_env_2.7.1/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
        from numpy.lib import add_newdoc
      File "/xchip/tcga/Tools/oncotator/onco_env_2.7.1/lib/python2.7/site-packages/numpy/lib/__init__.py", line 17, in <module>
        from . import scimath as emath
    ImportError: cannot import name scimath
  • ncamardancamarda DFCIMember, Broadie

    I also have this problem with oncotator --help after following these instructions. Please advise!

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