Thank you for the clarification.
I'll look into replacing BLAT with SHRiMP2, which is under a permissive
FOSS license. SHRiMP2 has comparable or superior performance across
different data types in multiple independent studies anyway. I just
wished I had not wasted three weeks scrubbing and refactoring BLAT's C
code.
David
On 2017-01-25 21:20, Martin Morgan wrote:
On 01/25/2017 08:12 PM, Dan Tenenbaum wrote:
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.
A very small number of Bioconductor packages have (or depend on
packages with) restrictive licenses, almost all for legacy reasons; a
few packages have gone to great lengths to ensure that their use of
otherwise restrictive code can be licensed in an open way. I'd be
extremely discouraging of a new package with a direct or implied
academic-only license.
There is some additional discussion on technical aspects of specifying
licenses in Writing R Extension section 1.1.2.
RShowDoc("R-exts")
Martin Morgan
Bioconductor
Dan
----- Original Message -----
From: "David J. H. Shih" <ds...@jimmy.harvard.edu>
To: "bioc-devel" <bioc-devel@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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