Re: [galaxy-dev] Installing toolshed repositories with set_environment dependency

23 Oct 2013

      Hello Saskia,

I haven't had a chance to look into this problem, but it's next on my list.  If both of the definitions you list worked in the past, then I believe they should still work.  It's possible tha t abut was introduced somewhere, and if so, I'll track it down and get it corrected.  I should be able to get back to you tomorrow on this one.

Thanks,

Greg Von Kuster

On Oct 23, 2013, at 11:34 AM, S.D. Hiltemann <s.hiltemann@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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