Hi Greg,

seems to work! Thanks!
Bjoern

> I believe this is fixed in 11184:d2b9f616e66c - at least everyting worked for 
> me.  However, committing to next-stable was a bit tweaky although I think all 
> is ok.  Please let me know if you see any problems.
> 
> Thanks!
> 
> Greg Von kuster
> 
> On Oct 30, 2013, at 4:09 PM, John Chilton <chil...@msi.umn.edu> wrote:
> 
> > I can verify augustus doesn't work correctly any longer, but I do not
> > get the same error. The package installs properly but set_environment
> > doesn't get handled.
> > 
> > As far as I can tell this changeset:
> > 
> > https://bitbucket.org/galaxy/galaxy-central/commits/ab9f5cb3acd8dcfe30fc5b92fc4a792c9815c877
> > 
> > Would break this functionality:
> > 
> >   <set_environment version="1.0">
> >       <environment_variable name="R_SCRIPT_PATH"
> > action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
> >   </set_environment>
> > 
> > (as documented on wiki and as appears in the augustus wrappers).
> > 
> > 
> > In particular these three lines:
> > 
> > elif elem.tag == 'set_environment':
> > env_var_name = env_var_elem.get( 'name', None )
> > if env_var_name:
> > 
> > Which have become:
> > 
> > elif elem.tag == 'set_environment':
> > env_var_name = elem.get( 'name', None )
> > if env_var_name:
> > 
> > Seem problematic. It looks like the set_environment element doesn't
> > have the name, it is the inner environment_variable elements that do.
> > This should probably be resolved before the next release.
> > 
> > -John
> > 
> > 
> > 
> > On Wed, Oct 30, 2013 at 10:10 AM, Bjoern Gruening
> > <bjoern.gruen...@gmail.com> wrote:
> >> Hi Greg,
> >> 
> >> sorry for the confusion. You answered to 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
> >> 
> >> If I search for that number I only find your fix for the repository
> >> action view. But I'm searching for the fix for ' Installing toolshed
> >> repositories with set_environment dependency'. Saskia posted that she
> >> gets that error:
> >> 
> >> NameError: global name 'env_var_elem' is not defined
> >> 
> >> And I can reproduce it with latest galaxy-central and
> >> http://toolshed.g2.bx.psu.edu/view/bgruening/augustus a repository that
> >> used to work, so I assume that is a regression.
> >> 
> >> Sorry for not being clear enough!
> >> Cheers,
> >> Bjoern
> >> 
> >> 
> >>> Hello Bjoern,
> >>> 
> >>> The changeset to which your link refers is the change that allows anyone 
> >>> that has write permission on a repository to reset all metadata on that 
> >>> repository from the "Repository Actions" pop-up menu on the
> >>> "View repository" page.  Previous to this change, this feature was 
> >>> restricted to the owner of the repository.  I committed this changeset to 
> >>> the next-stble branch and merged it into the central branch, so it is 
> >>> available in both.
> >>> 
> >>> I have just double-cheked using the central branch on my local 
> >>> development repository, and this feature is working as expected.  For 
> >>> example, if I have a repo owned by user test and only test has write 
> >>> permission on that repo, the user test1 cannot reset all metadata on the 
> >>> repo.  However, if user test grants write permission on the repo to user 
> >>> test1, then user test1 can immediately reset all metadata on the repo.
> >>> 
> >>> Can you let me know what steps you are taking and the behavior you are 
> >>> seeing that differs from this?
> >>> 
> >>> Thanks!
> >>> 
> >>> Greg Von Kuster
> >>> 
> >>> 
> >>> On Oct 29, 2013, at 1:03 PM, Bjoern Gruening <bjoern.gruen...@gmail.com> 
> >>> wrote:
> >>> 
> >>>> 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/
> > 
> > ___________________________________________________________
> > 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/
> > 
> 



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