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<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>  
|  Text<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>  |  
XML<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#> 
(full)<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>
⇝ 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     
[http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/media/plus.jpg]     
<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>  
view<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>
>>  <http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#> 
>> app_iter = self.application(environ, detect_start_response)
Module paste.recursive:84 in __call__     
[http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/media/plus.jpg]     
<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>  
view<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>
>>  <http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#> return 
>> self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__     
[http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/media/plus.jpg]     
<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>  
view<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>
>>  <http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#> return 
>> self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__     
[http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/media/plus.jpg]     
<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>  
view<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>
>>  <http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#> return 
>> self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request     
[http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/media/plus.jpg]     
<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>  
view<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>
>>  <http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#> body = 
>> method( trans, **kwargs )
Module galaxy.web.framework:229 in decorator     
[http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/media/plus.jpg]     
<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>  
view<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>
>>  <http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#> return 
>> func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:757 in 
manage_tool_dependencies     
[http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/media/plus.jpg]     
<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>  
view<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>
>>  <http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#> 
>> self.initiate_tool_dependency_installation( trans, 
>> tool_dependencies_for_installation )
Module galaxy.web.framework:229 in decorator     
[http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/media/plus.jpg]     
<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>  
view<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>
>>  <http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#> return 
>> func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:433 in 
initiate_tool_dependency_installation     
[http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/media/plus.jpg]     
<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>  
view<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>
>>  <http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#> 
>> tool_dependencies=tool_dependencies )
Module tool_shed.util.common_install_util:486 in handle_tool_dependencies     
[http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/media/plus.jpg]     
<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>  
view<http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#>
>>  <http://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593#> 
>> 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


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to