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:

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⇝ 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