Hello, I am trying to run HUMAnN on MetaPhlAn data, but HUMAnN does not recognise Cached database with clade-specific marker genes.
How can I install this database? Nukleotide and proteine databases are recognised. Thank you.
Just to clarify – you want a Data Manager to install these on a local Galaxy?
Go to the Tool Shed https://toolshed.g2.bx.psu.edu/ and run a search with the keyword “HUMAnN” to see the related tools, including data managers.
If that is what you did already, then something went wrong with the process. I would be curious about your configuration details, then at a higher level – have other data managers worked?
Let’s start there. 
Hello, datamanager does not install clade-specific marker genes database, it should be accessible from MetaPhlAn. The problem is this database should be named “vOct22_SGB” in data table metaphlan_database. I changed entry of this table and problem was solved.
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Great @KaunoSeptintasFortas ! Thanks for posting back what worked.
Did you have to add the metaphlan database to your history in order to use in HumanN?
Shure I am not. I never add databases to history because I am shure database must work from local data, not from history. I have 10+ students in class, it will be absolutelly imposible to work with him if every database everyone of them must add all databases to history 
Hi, adding to this post because it still seems to be relevant to this topic. Is the vOct22 chocophlan database the only one that is compatible with the Humann3.9 version on Galaxy? Is there a way to use the vJun23 database instead? THanks!
Hi @bethp
Can you share the sources links for all of this data since you are familiar with what fits together? Then we can make a request to get them updated. Thanks for helping us to keep all of this current! 
Hi @jennaj
I am the admin who manages galaxy instance that @bethp is using.
I added the Metaphlan database using Metaphlan datamanager. It created the database and added these entries
value name dbkey path db_version
mpa_vOct22_SGB_202403-31012025 MetaPhlAn clade-specific marker genes (mpa_vOct22_CHOCOPhlAnSGB_202403) mpa_vOct22_CHOCOPhlAnSGB_202403 /galaxy/galaxy-base/tool-data/metaphlan/data/mpa_vOct22_CHOCOPhlAnSGB_202403 SGB
mpa_vJun23_SGB_202403-03022025 MetaPhlAn clade-specific marker genes (mpa_vJun23_CHOCOPhlAnSGB_202403) mpa_vJun23_CHOCOPhlAnSGB_202403 /galaxy/galaxy-base/tool-data/metaphlan/data/mpa_vJun23_CHOCOPhlAnSGB_202403 SGB
Following the solution in this thread, I just copied the above entries and changed the value to satisfy the requirements for humann tool.
As made explicit in that, it just selects database with value that matches vOct22_SGB
Please let me know if you need more information.
–
Yash
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