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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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Environment variables in ModelSEEDbootstrap.pm #148

Closed samseaver closed 12 years ago

samseaver commented 12 years ago

Environment variables, such as ARGONNEDB, which are used by the MFAToolkit, but are set in ModelSEEDbootstrap.pm, are only set for the lifetime of the PERL job, and thus, when trying to debug/run MFAToolkit separately, one must explicitly set these environment variables.

Unfortunately for the user, if these aren't set, one only receives a seg fault for their trouble, so either the run_MFAToolkit.sh command does this, or its encoded, in turn, in the C++ code.

Or it can be added to bin/source-me.sh as an alternative.

samseaver commented 12 years ago

OK, I'm closing this issue, I just realized that the script created to run the toolkit, runMFAToolkit.sh, actually sources bin/source-me.sh, and thus the environment variables are there when run. I've just not run

source bin/source-me.sh

before starting up GDB