how to run a simulation with different forcing and initial conditions?

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If you're using CROCO_TOOLS, you may need to make modifications to the scripts (e.g. make_forcing, make_ini) to use different products as your boundary conditions. I am not familiar with JRA-55 but as long as the products you are using are available as regularly gridded netcdfs, the modifications required are probably minor (you will probably need to change some of the variable names and the routines dealing with missing values may need some checking). I've used ERA-I, ERA5, CMIP and CMEMS products as boundary conditions in the past and they were generally fairly painless to import with CROCO_TOOLS.