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:
<dependency> <groupId>org.broadinstitute.gatk</groupId> <artifactId>gatk-queue-extensions-distribution</artifactId> <version>3.5</version> </dependency>
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.