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



Hi Everyone,

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

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 ?

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>
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