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linsalrob / PyFBA

A python implementation of flux balance analysis to model microbial metabolism
http://linsalrob.github.io/PyFBA/
MIT License
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Error finding ModelSEEDDatabase variable #5

Open thh32 opened 6 years ago

thh32 commented 6 years ago

I have followed the instructions in creating the ModelSEEDDatabase variable as shown below;

thomas@Kiwi:~/PyFBA$ echo $ModelSEEDDatabase /home/thomas/PyFBA/ModelSEEDDatabase

However when I test the setup.py code the following occurs;

thomas@Kiwi:~/PyFBA$ python setup.py test Traceback (most recent call last): File "setup.py", line 7, in import PyFBA File "/home/thomas/PyFBA/PyFBA/init.py", line 5, in import PyFBA.gapfill File "/home/thomas/PyFBA/PyFBA/gapfill/init.py", line 13, in from .ecnumbers import suggest_reactions_using_ec File "/home/thomas/PyFBA/PyFBA/gapfill/ecnumbers.py", line 5, in MODELSEED_DIR = os.environ['ModelSEEDDatabase'] File "/usr/lib/python2.7/UserDict.py", line 23, in getitem raise KeyError(key) KeyError: 'ModelSEEDDatabase'

Any idea how to solve this?

cvagg commented 4 years ago

I am having the same issue, did you solve it?

travessny commented 3 years ago

I have the exact same issue. Could this be related to https://github.com/linsalrob/PyFBA/issues/4 or is it something else?

travessny commented 3 years ago

Found a solution. I no longer get this error if I export the variable as root user. su - export ModelSEEDDatabase=/home/user1/ModelSEEDDatabase