Hi Greg, do you mean that patch?
https://bitbucket.org/galaxy/galaxy-central/commits/all?search=83bed9c7dbbc I can reproduce that error and it is not fixed with latest galaxy-central, or did you only applied it to next-stable? You can test with my augustus repository if you like. http://toolshed.g2.bx.psu.edu/view/bgruening/augustus Thanks, Bjoern > Hello Saskia, > > > This was indeed a bug (not "abut" which was a spell checker spelling > error) which has been resolved in 11116:83bed9c7dbbc. This fix has > been committed to the next-stable branch and is currently running on > both the test and main Galaxy tool sheds. Thanks for reporting this > issue. > > > Greg Von Kuster > > > > On Oct 23, 2013, at 11:34 AM, S.D. Hiltemann > <s.hiltem...@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 > > > > > > > > ___________________________________________________________ > > 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/ > > > ___________________________________________________________ > 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/ ___________________________________________________________ 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/
