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: [email protected]
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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