Hello,

Yes $PATH is definitely exported in my .bash_profile.  I also tried a different test where I used <command>env &gt; $output1</command> and you wouldn't believe all my other environment variables are there perfectly except that $PATH is this incorrect one, it's like the tool runner purposely chose to reset $PATH.  Could it be because my $PATH is quite long?

-L

On Tue, Jul 13, 2010 at 7:23 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Leandro Hermida wrote:
Hi Nate,

Thank you for the suggestion, I tried it out and it doesn't seem to inherit any environment from the system user running Galaxy.

I made a test tool:

<tool name="Test" id="omics_data_miner_check_test" version="1.0.0">
   <command>echo \$PATH &gt; $output1</command>
   <inputs>
       <param name="input1" type="text" size="10"/>
   </inputs>
   <outputs>
       <data format="txt" name="output1"/>
   </outputs>
</tool>

And the result shown in Galaxy

/sbin:/usr/sbin:/bin:/usr/bin

Hi Leandro,

You may get different results if you put the echo in a shell script. Are you sure your $PATH variable is exported?

--nate



which is not my $PATH.



On Tue, Jul 13, 2010 at 6:53 PM, Nate Coraor <nate@bx.psu.edu <mailto:nate@bx.psu.edu>> wrote:

   Leandro Hermida wrote:

       Dear all,

       Sorry if I missed it, I looked in the list archives and couldn't
       find any mention of the topic.

       I am developing tools for Galaxy and thus running a Galaxy
       server from my within my home directory under my username. I
       have my own Perl installed in my home directory and this is in
       my $PATH, I don't use the system Perl, but when I run a Galaxy
       tool with <command interpreter="perl"> it is using the system
       Perl, as if my $PATH is not used at all.  Since the Galaxy
       server and tool runner is running under my username and it looks
       like it just forks off a call to "perl ...." when it forks why
       doesn't it use my Perl?


   Hi Leandro,

   When running locally, the shell invoked by Galaxy should inherit
   $PATH from its parent.  Can you create a basic script and run it as
   a tool that echos $PATH and see if it's what you expect?

   --nate


       best,
       Leandro


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