[Bioc-devel] Bioconductor package license: dependency on work under non-commercial license

David J. H. Shih dshih at jimmy.harvard.edu
Wed Jan 25 21:48:31 CET 2017


I'd like to ask whether Bioconductor will allow a dependency package 
under a non-commercial license:


I read the package guidelines: 
http://bioconductor.org/developers/package-guidelines/#license but it 
does not address this question.

I am putting together a package for somatic variant filtering. One of 
the filters involve re-aligning the supporting reads using a heavily 
refactored version of BLAT: MLAT (https://github.com/djhshih/mlat). BLAT 
remains under a license that restricts commercial users. Although the 
original license mentions no restriction on derivative work, I contacted 
the author, and he maintains that the non-commercial license applies to 
derivative works. Eventually, I'll probably replace BLAT (with another 
aligner like SHRiMP2, which appears to have superior sensitivity and has 
a permissive license), but I was wondering how I might be able to 
assemble my package in the short term.

Here is my plan:

1. Create a BLAT/MLAT package under BLAT's non-commercial license.
2. Create the main package under GPLv3 that optionally depends on BLAT.

Will Bioconductor permit a optional dependency package under a 
non-commercial license?

Best regards,

Postdoctoral Research Fellow
Department of Biostatistics and Computational Biology, Dana-Farber 
Cancer Institute
Department of Biostatistics, Harvard T.H. Chan School of Public Health
Cancer Program, Broad Institute
3 Blackfan Circle, CLS-11082
Boston, MA 02115

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