I'm getting this same error on my mac osx build. Any luck solving this issue? 
Primer3/eprimer3 issue:
Error: thermodynamic approach chosen, but path to thermodynamic parame
+ters not specified

[download]
From: http://www.mcardle.wisc.edu/mprime/help/primer3/primer3_manual.htm#globalTags

PRIMER_THERMODYNAMIC_PARAMETERS_PATH (string; default ./primer3_config)

This tag specifies the path to the directory that contains all the parameter files used by the thermodynamic approach. In Linux, there are two default locations that are tested if this tag is not defined: ./primer3_config/ and /opt/primer3_config/. For Windows, there is only one default location: .\primer3_config\.

I put the primer3_config in my PATH in bin and still cannot solve this issue:

I even did 

export PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/Users/jared/Downloads/pri
+mer3-2.3.2/src

[download]
and 
export PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/Users/jared/Downloads/pri
+mer3-2.3.2/src/primer3_config

[download]
to no avail.

In reply to Re^5: Primer3 - BioPerl by datz
in thread Primer3 - BioPerl by blarsen20

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