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Re: VirusSeeker: RepeatMasker missed in dependencies (Was: VirusSeeker - sorting the Downloads section)



Hi Étienne,

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:
> 
> 	http://www.repeatmasker.org/RMDownload.html

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:
> 
> 	https://wiki.debian.org/DFSGLicenses#Open_Software_License_.28OSL.29_v1.1
> 	https://www.gnu.org/licenses/license-list.html#OSL
> 
> 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.

Kind regards

      Andreas.

> merkys@debian.org, 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 <etienne.mollier@mailoo.org>
> Fingerprint:  5ab1 4edf 63bb ccff 8b54  2fa9 59da 56fe fff3 882d
> Help find cures against the Covid-19 !  Give CPU cycles:
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