Hi,
Could this be related to the fact that galaxy is not seeing the tools that are 
installed in /usr/local/bin?? 
I'm on latest_2015.01.13 and since the two last upgrades I saw that 
interproscan and bsmap were not found by galaxy. Both are installed in 
/usr/local and when invoked on the command line, as the galaxy user, they work 
perfectly well. Before the last two upgrades both worked from within galaxy.
Cristian
> Date: Wed, 21 Jan 2015 10:11:43 -0500
> From: jmchil...@gmail.com
> To: wolfgang.ma...@biologie.uni-freiburg.de
> CC: galaxy-...@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] PATH set in tool env.sh leaking through to  
> set_metadata.py
> 
> So the tool dependency stuff didn't change - but the local job runner
> now behaves like the other job runners (DRMAA, PBS, etc...) so you
> have uncovered a bug for all of them I think. Is this a tool shed tool
> or a locally created dependency?
> 
> I need to think about how to solve this more generally but if you want
> a quick work around - I think it would work to just replace "python"
> in $GALAXY_ROOT/set_metadata.sh with a  hard-coded path to Galaxy's
> python or perhaps just "python2".
> 
> Sorry for the inconvenience and thanks for bringing this to our attention.
> 
> -John
> 
> On Tue, Jan 20, 2015 at 12:52 PM, John Chilton <jmchil...@gmail.com> wrote:
> > Are you using the local job runner (this will be the case if you
> > haven't explicitly configured something like pbs or DRMAA in your
> > job_conf.xml file)?
> >
> > -John
> >
> > On Tue, Jan 20, 2015 at 12:34 PM, Wolfgang Maier
> > <wolfgang.ma...@biologie.uni-freiburg.de> wrote:
> >> On 01/20/2015 06:20 PM, Wolfgang Maier wrote:
> >>>
> >>>
> >>> I have not seen this error before (I believe not with latest_2014.10.06)
> >>
> >>
> >> update: confirmed this now. It's enough to hg update to latest_2014.10.06
> >> and things are working again.
> >>
> >> The difference is that when building the dependency shell command the 
> >> latest
> >> release seems to put the call to set_metadata.sh into that command, while
> >> before it seems it was run separately.
> >>
> >>
> >> Wolfgang
> >>
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