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Using protected Queue code in open source package (Biopet)

Last week I did have a chat with @Geraldine_VdAuwera in Edinburgh about our split licence in our project. This only because we rely on some protected code of the queue extensions of the GATK walkers. To prevent problems I did split out repository in public and protected just like you are doing in GATK 3 right now. This prohibit us to distribute our jar.

Out repository is available here: https://github.com/biopet/biopet

This is the module that causes the problem:


We don't include GATK itself in our project, the user should download this themselves and supply this in a config file.

It would be better to get rid of this split licence so we can get full open source. This also allows of to distribute our jar. As discussed with @Geraldine_VdAuwera it might be possible to get permission to use the protected modules in our public code. Before I do this I would like a explicit permission from Broad to do this to prevent any law issues.

So would it be possible to get this permission? Thanks already for looking into this.


Issue · Github
by Sheila

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Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @pjvthof,

    I'm still in the middle of the Oxford workshop so I can't yet look at your question in detail, but will do so when I'm back in Boston later this week.

    In preparation for that, can I ask you to please clarify the following: do you need to be able to distribute the protected code, the jar file, or both?

    As things stand we have a clear path to allowing you to distribute the jar file; that is fairly straightforward due to recent developments as we discussed last week in Edinburgh. Distributing protected code is a much more thorny issue. If what I remember of what you wanted to do is correct, we may need to seek a technical workaround -- in any case we will do what we can to help.

  • pjvthofpjvthof NLMember

    The protected code of GATK is only needed once to install the compiled jars in a local maven repository because the GATK modules are not in a public maven repository as far as I know. This is only required as a developer and for this we use: https://github.com/broadgsa/gatk-protected

    This means that the code itself will be not included when distributing. All that non-developers need is the jar file of Biopet. This jar will include the modules of GATK where it depends on. The source code of GATK will be not distributed as a jar and is not included in our git repository.

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