Why does blast not work w/ Pathway Tools?

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Pathway Tools uses the system's PATH environmental variable to find where external programs are installed. By default, when BLAST is installed, it may only add the path to blast binaries to the user's default path, not the system's default path. Please review the Pathway Tools BLAST installation guide for details: http://bioinformatics.ai.sri.com/ptools/installation-guide/released/blast.html

Once BLAST is added to the default search path, you'll need to restart Pathway Tools for it to find the blast executables.