hallamlab / metapathways2

MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds
http://hallam.microbiology.ubc.ca/MetaPathways/
33 stars 14 forks source link

template_config.txt forces the appending of MP install directory to executable paths #103

Open katharinedickson opened 3 years ago

katharinedickson commented 3 years ago

When running MetaPathways, I'm running into a problem properly setting the right pathways to existing executables on my machine.

In template_config.txt, my Perl executable setting is PERL_EXECUTABLE '/usr/bin/perl' because this is what I get when I type 'source MetaPathwaysrc'.

However, it appears that the config file forces the appending of the directory in which I've installed MetaPathways into the path for the Perl executable, as per the following (/home/dickson/metapathways2-2.5.1/ is the directory for my MP installation):

ERROR:Path for "PERL_EXECUTABLE" is NOT set properly in configuration file "/home/dickson/metapathways2-2.5.1/config/template_config.txt"
5.Currently it is set to "/home/dickson/metapathways2-2.5.1//usr/bin/perl"

How can I fix this?