The current GATK version is 3.2-2

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Bug Bulletin: The GenomeLocPArser error in SplitNCigarReads has been fixed; if you encounter it, use the latest nightly build.

# (howto) Install and run Oncotator for the first time

edited July 29

Both packages are simple tar files that can be expanded using the following commands:

$tar zxvf oncotator-1.3.0.0.tar.gz$ tar zxvf oncotator_v1_ds_June112014.tar.gz


This will produce two directories called oncotator-1.2.0.0 and oncotator_v1_ds_June112014, respectively. Move to the oncotator-1.3.0.0 directory by doing:

$cd oncotator-1.3.0.0  ## 2. Set up your Python environment and install dependencies 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). ## 3. Install Oncotator 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 oncotator and 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 hg19 reference.

Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

Tagged:

• Posts: 12Member

An error occurred while installing Oncotator.

error: Setup script exited with error: command 'gcc' failed with exit status 1

What do i do ?

@pmint, have you looked at the compiler requirements in this document?

Geraldine Van der Auwera, PhD

• Posts: 1Member

An error occurred while installing Oncotator. Yachtmaster

Geraldine Van der Auwera, PhD

• xiuque88Posts: 2Member

Hi Geraldine,

Thanks you and your team at Broad for providing a local installation of oncotator. Could you provide the checksum for the datasource corpus ? I want to ensure that the download went perfectly.

Thanks! Cheers.

• xiuque88Posts: 2Member
edited July 16

Good day,

I was running the test set and a got a series of warnings :

            014-07-17 03:25:13,066 WARNING [oncotator.output.TcgaMafOutputRenderer:197] Entrez Gene ID was zero, but Hugo Symbol was not Unknown.  Is the HGNC and/or Transcript datasource complete?


Cheers

Post edited by xiuque88 on

Geraldine Van der Auwera, PhD

• Posts: 1Member

Hi Geraldine,

I have the same issue. The link specified above is broken. Would you please provide a new one for me? I really appreciate it.

Best, Joon

Geraldine Van der Auwera, PhD

• ChinaPosts: 1Member

I was install oncotator and got a error: ERROR: Could not load pysam. Some features will be disabled (e.g. COSMIC annotations) and may cause Oncotator to fail. No handlers could be found for logger "root". I used the virtual environment script and the pysam-0.7.5 package have been successfully installed. I was confused why got this error when I test the oncotator. Can you give me some suggestion?

Hi @vguest‌,

Can you post the output that was generated during the installation process?

Geraldine Van der Auwera, PhD

• Posts: 4Member

We love having the local installation of Oncotator because of the improved ease of use and convenience. We do trip up ourselves from time to time when we forgot whether the dozens of output files contain canonical or best effect annotations or that the --tx-mode flag was set to "EFFECT" or not. Can you add as a future enhancement a text string in the output file to label the output as either Canonical or Best Effect? The text string does not have to be in the column headers but wherever it is sensible for you to put it.

Hi @chung2000, we've put this in as a feature request. In the meantime, one way to keep track of this is to check the run logs.

Geraldine Van der Auwera, PhD

• Posts: 4Member

Thank you @Geraldine_VdAuwera. While the run logs are excellent records for when, where, and how the --tx-mode flag was set, all is lost when the Oncotator output files gets passed around to other people in our group or to other organizations because we rather not send the run logs to those people.

@chung2000 I understand, it is awkward to rely on log files. This will be implemented in an upcoming version -- we'll make an announcement when the next release is ready.

Geraldine Van der Auwera, PhD