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computational-metabolomics / metfrag-galaxy

Metfrag for Galaxy
GNU General Public License v3.0
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implement local db / metfrag as conditional #5

Closed bernt-matthias closed 5 years ago

bernt-matthias commented 5 years ago

Since either a local db or a metfrag db has to be chosen this shoud be realised with a conditional.

korseby commented 5 years ago

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

korseby commented 5 years ago

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.

Tomnl commented 5 years ago

@RJMW we can set this local database system up on one of the Birmingham virtual machines

bernt-matthias commented 5 years ago

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)?

Tomnl commented 5 years ago

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:

@RJMW

RJMW commented 5 years ago

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?

Tomnl commented 5 years ago

This is now implemented following #8