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/
> > 
> > 
> > 
> 



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