On Tue, Jul 13, 2010 at 7:06 PM, John Brunelle <
john_brunelle@harvard.edu <mailto:
john_brunelle@harvard.edu>> wrote:
Hi Leandro,
A lot of tools that are perl or python scripts will have the shebang
line hardcoded to the system version, e.g.:
#!/usr/bin/perl
If you change that to:
#!/usr/bin/env perl
it'll pick up the version in your path. For example, we had to do
this with tophat (python).
However, that only applies to scripts that are run directly -- I'm
not sure how Galaxy tool configs and the interpreter parameter work.
Best,
John
On Tue, 13 Jul 2010, 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?
best,
Leandro