Hi Étienne, On 2020-04-09 21:25, Étienne Mollier wrote: > On a side note, there is a page[3] referring to all sorts of > different locations for getting NCBI NT/NR/taxonomy and virus > nucleotide and protein databases. This is also in this chapter > that the configuration of VirusSeeker is described. For the > moment, configuring consists in hopping into Perl scripts and > setting paths in perl variables accordingly. I don't know if > those databases would require additional packaging (if even > allowed), or some kind of mecanism to pull it on the system. > But I'm under the impression that they might be necessary for > the software to be useful. They are located in a whole set of > different locations. > > [3] https://wupathlabs.wustl.edu/virusseeker/installation/install-databases/ I am not aware of databases packaged for Debian. Most likely they the user is expected to download them and give their paths on a filesystem via a configuration file or environment variable. So options seem to be those: 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. Option 1. would be easier to implement using simple patches. Option 2. would need much more patching. It would be the best to convince the upstream to make their software configurable via option 2., this way we would not need to maintain patches. Hope this helps, Andrius
Attachment:
signature.asc
Description: OpenPGP digital signature