Re: VirusSeeker: RepeatMasker missed in dependencies (Was: VirusSeeker - sorting the Downloads section)
On Thu, May 07, 2020 at 11:24:00PM +0200, Étienne Mollier wrote:
> I've been quietly chiseling the packaging of virusseeker-virome,
> but I missed the proper RepeatMasker dependency in the initial
> list; Debian provides a few packages related to that software,
> and I mistakenly thought it was available already. For
> reference, it is the software available at:
Thanks a lot for checking.
> Unfortunately, I understand that it is licensed under OSL 2.1,
> and that this license does not look DFSG compliant, nor seems
> compatible with the GPL:
> At some point, I wondered if it would be possible to get
> RepeatMasker into "non-free", and having VirusSeeker into
> "contrib" then, but I'm not sure that this is legally doable
> since VirusSeeker is GPL.
> Have you already met similar situation in the past ?
> If so, how has it been dealt with ?
Hmmm, I do not remember but non-free is ugly for several technical
reasons (no autobuilders, no autopkgtests, no QA checks etc.) Thus
the first thing I do is contacting upstream to consider changing
their license. Would you mind doing so? If yes, I would consider
mentioning our COVID-19 sprint and that a free license would support
us in our fight against the pandemic.
> email@example.com, on 2020-04-10 07:40:42 +0300:
> > 1. Replace hard-coded database paths with environment variables, say,
> > VIRUSSEEKER_NCBI_NT. Then prior to running the VirusSeeker the user
> > would need to download the databases and set these environment variables
> > to their locations.
> > 2. Make their paths configurable via a configuration file (under /etc,
> > possibly) listing paths for the databases. After installing the Debian
> > package, the user would have to edit this configuration file to point to
> > the database locations.
> Hi Andrius,
> Thank you for your thoughts, even if I'm a bit late. Reading
> through the script, even using environment variables, there is
> a quite big share of hard-coded paths, so would probably attempt
> to contact upstream in any case.
> Kind Regards,
> Étienne Mollier <firstname.lastname@example.org>
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