On Thu, Feb 26, 2015 at 1:35 PM, Pierre Lindenbaum
<pierre.lindenb...@univ-nantes.fr> wrote:
>> You'll need to white list the semi-colon which Galaxy has replaced as a
>> security precaution (user free text can be exploited). See <sanitizer> here:
>> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter
> Thanks: adding :
>        <sanitizer>
>               <valid initial="string.printable">
>                      <remove value="&apos;"/>
>                 </valid>
>          </sanitizer>
> fixed the probem.


>> Could you confirm if the environment variable is being set now?
> Hum the variable is not set , ...

How was the tool installed into your Galaxy? Was it via a (local)
Tool Shed which would have processed the tool_dependencies.xml

Or, have you manually added your tool XML to Galaxy by hand
(which is what I still do when developing a new tool)? In this
case you'd have to manually set the environment variable.
(I delay messing about with dependencies until after the tool
works locally, and then test them via the Test Tool Shed.)

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