Hello Saskia,

This was indeed a bug (not "abut" which was a spell checker spelling error) 
which has been resolved in 11116:83bed9c7dbbc.  This fix has been committed to 
the next-stable branch and is currently running on both the test and main 
Galaxy tool sheds.  Thanks for reporting this issue.

Greg Von Kuster


On Oct 23, 2013, at 11:34 AM, S.D. Hiltemann <s.hiltem...@erasmusmc.nl> wrote:

> I updated my Galaxies to the latest version today, and when I try to install 
> a toolshed repository which defines an environment variable via the 
> <set_environment> tags in the tool_dependencies.xml file, I get an error (see 
> below).
> 
> tool_dependencies.xml:
> 
> <?xml version="1.0"?>
> <tool_dependency>
>     <set_environment version="1.0">
>         <environment_variable name="CONDEL_SCRIPT_PATH" 
> action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>             
>     </set_environment>   
> </tool_dependency>
> 
> (before the update these repositories installed without problems)
> 
> ..doing the same as an action within a package dependency does still work, so 
> for now I have just changed the tools I needed to set the environment this 
> way, e.g.:
> 
> <tool_dependency>
> <package name="condel" version="1"> 
>         <install version="1.0">
>             <actions>    
>                 <action type="set_environment">
>                     <environment_variable name="CONDEL_SCRIPT_PATH" 
> action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> 
>                 </action>                                           
>             </actions>
>         </install>
>         <readme>
>             Set condel environment variable
>         </readme>
>     </package>      
> </tool_dependency>
> 
> Is this the preferred way of doing it, and should I change all my tools this 
> way? or should both ways still be working?
> 
> Saskia
> Error Traceback:
> 
> View as:   Interactive  |  Text  |  XML (full)
> ⇝ NameError: global name 'env_var_elem' is not defined
> URL: 
> http://galaxy.trait-ctmm.cloudlet.sara.nl/admin_toolshed/manage_tool_dependencies?repository_id=b847e822bdc195d0&operation=install
> Module weberror.evalexception.middleware:364 in respond          view
> >>  app_iter = self.application(environ, detect_start_response)
> Module paste.recursive:84 in __call__          view
> >>  return self.application(environ, start_response)
> Module paste.httpexceptions:633 in __call__          view
> >>  return self.application(environ, start_response)
> Module galaxy.web.framework.base:132 in __call__          view
> >>  return self.handle_request( environ, start_response )
> Module galaxy.web.framework.base:190 in handle_request          view
> >>  body = method( trans, **kwargs )
> Module galaxy.web.framework:229 in decorator          view
> >>  return func( self, trans, *args, **kwargs )
> Module galaxy.webapps.galaxy.controllers.admin_toolshed:757 in 
> manage_tool_dependencies          view
> >>  self.initiate_tool_dependency_installation( trans, 
> >> tool_dependencies_for_installation )
> Module galaxy.web.framework:229 in decorator          view
> >>  return func( self, trans, *args, **kwargs )
> Module galaxy.webapps.galaxy.controllers.admin_toolshed:433 in 
> initiate_tool_dependency_installation          view
> >>  tool_dependencies=tool_dependencies )
> Module tool_shed.util.common_install_util:486 in handle_tool_dependencies     
>      view
> >>  env_var_name = env_var_elem.get( 'name', None )
> NameError: global name 'env_var_elem' is not defined
> 
> 
> 
> From: S.D. Hiltemann
> Sent: Friday, August 02, 2013 11:19 AM
> To: galaxy-dev@lists.bx.psu.edu
> Subject: Toolshed repository update error
> 
> I am working on putting a tool into the toolshed. I have a bash script 
> wrapper. I uploaded the first version fine, but when I wanted to upload a 
> revision, some unwanted characters are inserted around the revised function 
> of my code (see bottom) ..the inserted "<<<<<< local" etc strings are causing 
> my script to fail of course. How can I prevent this from happening? 
> 
> Saskia
> 
> 
> snippet of the code:
> 
> 
>     if [[ ! -s $rfile ]] 
>     then           
>         dummycol=${addcols:2}
>         outputcol=${dummycol//",B."/"    "}
> <<<<<<< local
>         echo -e 
> "${col_chr_name}\t${col_start_name}\t${col_end_name}\t${col_ref_name}\t${col_obs_name}\t$outputcol"
>  > $rfile    
>         cat $rfile        
> =======
>         numcommas=`echo "$addcols" | grep -o "," | wc -l`
>         echo "numcolums: $numcommas"
>         
>         awk 'BEGIN{FS="\t";OFS="\t"}{
>                 if(FNR==1)
>                     print $0,"'"$outputcol"'"; 
>                 else{
>                     printf $0
>                     for(i=0;i<="'"$numcommas"'"+1;i++)
>                         printf "\t"
>                     printf "\n"
>                 }
>             }END{}' $ofile > tempofile
>             
>             mv tempofile $ofile
>         
>         return
> >>>>>>> other
>     fi
> 
> 
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