Hi, Dear all, I am trying to integrate a perl script to GALAXY, and here are the problems. I have a tool configuration xml file called abc.xml located at tools/myTools directory, which calls a perl scripts called toolExample.pl. 1 <tool id="abc" name="abc"> 2 <command interpreter="perl">toolExample.pl $input $output</command> 3 <inputs> 4....... 5...... Inside the toolExample.pl, I am using some linux system command such as "wc" and also "BEDTools/windowBed". The BEDTools executables are configured correctly in my local linux machine, and when I type "which windowBed" it can give me back the path correctly. When I run toolExample.pl outside galaxy in the terminal, everything looks correct; but when I run galaxy, it gave me the nonsense results ( all 0) and it seems that GALAXY has problems in recognizing either the windowBed excutable file or the linux system command "wc" or maybe both. To let GALAXY recognize "windowBed", I tried to put the windowBed executable copied to myTools directory and add the following <requirements>tags to the abc.xml file, but it doesn't seem to be working. ..... <requirements> <requirement type="binary">windowBed</requirement> </requirements> .... Could anyone please help me figure out what was wrong? How can I fix the problem? Thank you very much in advance! Best, Jenny