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

Dan Tenenbaum dtenenba at fredhutch.org
Thu Jan 26 02:12:40 CET 2017

I can't speak to the license question (I'd guess the answer is no) but I am pretty sure that any dependencies of a Bioconductor package have to be available on CRAN or in Bioconductor itself. So you can't depend on packages that are only in GitHub.


----- Original Message -----
> From: "David J. H. Shih" <dshih at jimmy.harvard.edu>
> To: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Wednesday, January 25, 2017 12:48:31 PM
> Subject: [Bioc-devel] Bioconductor package license: dependency on work under	non-commercial license

> Hello,
> I'd like to ask whether Bioconductor will allow a dependency package
> under a non-commercial license:
> https://github.com/djhshih/mlat/blob/master/LICENSE_blat.txt
> 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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