java - Tomcat application cannot see my $PATH variable -


there tomcat application thats been running on 1 of our servers (written else in our lab gone). know little tomcat , how works, i've narrowed problem down 2 solutions.

the error i'm getting on webpage is:

java.io.ioexception: cannot run program "hmmtop": error=2, no such file or directory

server information tomcat version jvm version jvm vendor os name os version os architecture apache tomcat/6.0.26 1.6.0_65-b14-462-10m4609 apple inc. mac os x 10.6.8 x86_64

before os x update script worked fine. cannot find program called 'hmmtop'. program, 'hmmtop' located : /users/saierlab/bin/hmmtop, , exist.

solution 1) tried changing file named 'myfile.java' use absolute path, looks this:

string command = "/users/raven/bin/hmmtop -if=" + this.filename + ".fa";

this file located in "/usr/local/tomcat/webapps/avehas/web-inf/classes" however, when change nothing reflected. i'm not sure how compile these changes. tried running javarc myfile.java , gave me hundreds of errors, don't think thats how go this. mind i've never used tomcat before.

i don't have original war file or anything, , whats in directory have pertaining particular program.

solution 2) if can't quite figure out how re-compile script, there way can tell tomcat aware of /users/raven/bin/ directory in $path variable?

thank you!


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