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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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getting carveme to run #46

Closed lavik17 closed 5 years ago

lavik17 commented 5 years ago

I've installed carveme using pip. I then realized that I did not install CPLEX so I've installed CPLEX and CPLEX python api. Diamond was pre-installed.

When I ran carveme I got an error saying that it cannot find cplex, so I used a solution from another issue report: export PYTHONPATH=$PYTHONPATH:/local/CPLEX_Studio_Community128/cplex/python/2.7/x86-64_linux/ which is the path where CPLEX is found on my drive. However, now when I run carveme, I get a carveme: command not found I removed carveme with pip uninstall and re-installed it, but still get the same error.

any ideas how to solve this?

rdmtinez commented 5 years ago

try running carve

cdanielmachado commented 5 years ago

Exactly. First carveme_init the first time you run the tool. And afterward just carve [genome] every time.

But I find it strange that you need to change your PYTHONPATH. When you run python setup.py install inside that folder it should install the cplex api inside your current python environment.