BINFBINROOT Variable

[wmaguire-gladstone]

MonkeyPipeline/bananas_agw.pm

Lines 40 to 47 in e010cd6

	(defined($ENV{BINFBINROOT}) and length($ENV{BINFBINROOT}) >= 1) or confess "-----------\n[ERROR]: You need to define the UNIX system-wide environment variable 'BINFBINROOT' (for 'bioinformatics binary root') in your ~/.bashrc file before you can run Monkey.\nHere is an example of something you can add to the ~/.bashrc: export BINFBINROOT=/data/applications/2015_06/bin \n(Make sure to log out and log back in after you set that, or type 'source ~/.bashrc' to reload the bash config file). If you add that and it doesn't work, try checking the value of 'echo \$BINFBINROOT' and make sure that actually prints the proper path.\n------------ ";
	our ($GLOBAL_BIN_DIR) = $ENV{BINFBINROOT}; # "/data/bin/2015_06"; # <== note: hard-coded, and NOT THE "monkey" /bin dir with the perl scripts in it! (That's the 'monkeyPoo' directory)
	if (not -d $ENV{BINFBINROOT}) {
	warn("[WARNING]: Your environment variable 'BINFBINROOT' (for 'bioinformatics binary root') was not set to a valid directory that already exists! You will need to properly set the 'BINFBINROOT' in your ~/.bashrc file. You can check to see what this variable is set to by typing 'echo \$BINFBINROOT' on the command line. It should be a directory with a bunch of programs in it. The current (probably incorrect) one is set to this value: <$GLOBAL_BIN_DIR> (which does not seem to be a valid directory)");
	confess "Failure to find a valid directory with binaries in it, which we expect to be specified in the 'BINFBINROOT' environment variable.\nSee text above for details.\nIn other words---your environment variables in your ~/.bashrc are NOT set up correctly.";
	}

I found that this BINFBINROOT (bioinformatics bin root) variable. We don't need to change the code, but this is referencing a system-wide environment variable that Alex had setup and informed users to add to their bashrc file. It's value was /data/bin/2015_06 but should now be set to /wynton/group/gladstone/third_party/monkey_path