Comments (7)
@RJMW we can set this local database system up on one of the Birmingham virtual machines
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For that you need a local db running. We should have a Dockerfile floating around somewhere here https://github.com/ipb-halle/MetFragRelaunched/tree/containerize
I think we should implement this in the rewrite of the tool
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The Dockerfile and instructions to build the local pubchem mirror database can be found here: https://github.com/c-ruttkies/container-metchemdata
@sneumann also has recent kubernetes deployment yamls.
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Currently in the tool the "local data base" is just a csv file.
Most frequently the Galaxy tool-data loc files specify files, but its definitely possible to specify a connection string.
For my curiosity: the DB you are referring to is some SQL DB? In the docker it seems to be postgres in the backend, but could be any DB (sqlite)?
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hi @bernt-matthias,
We should still keep the option to have a "local database" that is just a csv file, and it should be realised as a conditional - like you mentioned in the original issue message.
The database @korseby is referring to is a local PubChem database (With a few modifications - called MetChem) and can be used in replace of doing the API calls to the public PubChem instance. See xml and script.
So, I will update Galaxy tool and script here for the following database options:
- PubChem
- KEGG
- ChemSpider - if still working
- MetChem
- (and provide option for user to choose IP address of local instance)
- LocalCSV
- (and provide option for user to choose an uploaded CSV file)
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I agree @Tomnl.
Examples for "LocalCSV" are available from here:
https://msbi.ipb-halle.de/~cruttkie/databases/
https://msbi.ipb-halle.de/~cruttkie/metfrag/example_local_inchi_file.txt
@korseby are there any more up-to-date csv files available?
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This is now implemented following #8
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