MetaboHUB-MetaToul-FluxoMet / RTMet

RTMet is a data workflow to process FIA-MS data coming from a bioreactor, find metabolites and fluxes, and send a feedback command to the system.
https://rtmet.readthedocs.io
GNU General Public License v3.0
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Replace homemade annotation script with W4M's `lcmsmatching` #12

Open elliotfontaine opened 3 months ago

elliotfontaine commented 3 months ago

https://github.com/workflow4metabolomics/lcmsmatching

Steps:

elliotfontaine commented 1 month ago

See discussion in https://github.com/workflow4metabolomics/lcmsmatching/issues/68.

Replacing the mzmatch junk script used by our workflow by the lcmsmatching R script won't be straightforward. The latter doesn't work with current versions of its core dependency biodb. One approach would be to partially reimplement lcmsmatching using biodb 1.10.0, and following what's inside vignettes: