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: Interactivehttp://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593# | Texthttp://galaxy.trait-ctmm.cloudlet.sara.nl/_debug/view/1382536593# | XMLhttp://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_depende... 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# viewhttp://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# viewhttp://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# viewhttp://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# viewhttp://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# viewhttp://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# viewhttp://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# viewhttp://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# viewhttp://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# viewhttp://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# viewhttp://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