add checkm2 #6542
add checkm2 #6542
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remove dbkey column rename tables
and add working output assertions as comment
| #The <version> column indicates the checkm2 version that generated the database | ||
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| #diamond_db_1.0.2 Diamond database 1.0.2 /mnt/galaxyIndices/Checkm2_database/uniref100.KO.1.dmnd |
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Is this really a diamond DB?
If so, this is interesting ... should we have a general Diamond location file and DM? with some tag for different tools?
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I think so. And I agree that it would be interesting.
But it would be good to know and store the diamond version that has been used to generate it, or? Seems difficult to find out from the sources. The tool just downloads the latest version from zenodo (and I could not even find the link). Let me check if diamond dbinfo could help.
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Nice:
> diamond dbinfo -d uniref100.KO.1.dmnd
diamond v2.0.4.142 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Database format version = 3
Diamond build = 142
Sequences = 6518230
Letters = 2584051404
Should we do this? Add columns tool, db_format_version, diamond_build?
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Do we need diamond_build? But yes, we should do that :)
Thanks!
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@astrovsky01 do you think you can work on this?
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Yes. I had to get something up and running somewhere I could test it, but I just got it going
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After some digging, I found that Checkm2 doesn't actually work with all diamond databases. It has an internal checksum to make sure it's the specific one from the database download command:
as such, I think that while it would be good to have the general Diamond db data manager, having a specific one for checkm2 is also a good idea
FOR CONTRIBUTOR: