ressy
commented
3 years ago I haven't been doing metagenomics projects for a long while myself so I'm not sure how much use this extension is getting, but I see what you mean. The bioconda package is still there but --install fails because of the missing tarball on bitbucket.
For the moment maybe it'd be simplest to try to get the older version running by supplying the older database, but I'm not sure where to find it now. I poked around in my files a bit to see if I have a copy of the old database lying around but it doesn't look like it. At least one person asked a similar question last year on their forum ("how and where do i get the legacy database") in a slightly different context:
https://forum.biobakery.org/t/how-to-install-metaphlan2-legacy-database/171
I don't follow the bit about an older version of the conda-provided package providing a database, though. I don't see any sign of one when I install version 2.7.7 from bioconda and --install dumps a 404 web page from bitbucket into what's supposed to be the tarball.
In the long run, yeah, getting it going with Metaphlan3 would be best. All of Sunbeam could use some developer attention, really, but I think we've all been pulled in different directions or dispersed to different organizations so it's a challenge. Personally I've been hoping to find some time to address some of the open issues but just haven't been able to for a while. (I realize that's not really an answer to your question but hopefully at least it gives some context on where things stand.)
TakacsBertalan
I don't know if this tool is still being monitored or developed, but it needs some update. I try to use it as part of Sunbeam, but the original Metaphlan2 project is removed from bitbucket, which means that this tool can't work properly in it's current form. It tries to download the metaphlan database from bitbucket in the first step and it fails. This breaks the whole process. Is there a way to make the tool to work for Metaphlan3? Thanks