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ModelSEED / Model-SEED-core

The Model SEED is a tool for building, curating, and analyzing gonome-scale metabolic models. Visit the Model SEED homepage for installation instructions and full feature documentation.
http://bionet.mcs.anl.gov/index.php/Model_SEED_Homepage
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loadmodelfromfile issues #43

Closed samseaver closed 13 years ago

samseaver commented 13 years ago

I've not tried this in the BIO environment, but locally:

1) The -biomass parameter doesn't work, it keeps looking in the same location (./data/MSModelFiles)

2) The -filename parameter works, but if it is not used, then the filename that it looks for must have the user index in the filename, ie:

data/MSModelFiles/iJR904.45632.tbl1

instead of

data/MSModelFiles/iJR904.tbl

3) The overwrite function works for sake of documentation, but if the script fails the first time (ie can't find biomass file) it doesn't roll back the inserted data, so the next time you run it, even though it "failed" you still have to overwrite. This can be confusing.

tammyk commented 13 years ago

Whenever I try to load my model it says it "could not find biomass specification file" (even tho the biomass file is in MSModelFiles and I even load it to the database before loading the model). I was wondering where I can find the user index number, so maybe if I try to include the path with the user index it would work.

samseaver commented 13 years ago

No longer an issue