Hello,
Yes $PATH is definitely exported in my .bash_profile. I also tried a different test where I used <command>env > $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 > $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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