This problem should be fixed in change set 6672:e38a9eb21336, which is now 
available in our central repo.  Thanks for reporting this, and let me know if 
you discover other issues.

Greg


On Feb 6, 2012, at 7:54 AM, Bossers, Alex wrote:

> Greg,
> Exactly as you say. You cannot insert the repository tool when it’s an empty 
> section.
> Sorry for being unclear.
> Alex
>  
> Van: Greg Von Kuster [mailto:g...@bx.psu.edu] 
> Verzonden: maandag 6 februari 2012 12:57
> Aan: Bossers, Alex
> CC: Ira Cooke; galaxy-dev@lists.bx.psu.edu Dev
> Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
>  
> Hello Alex,
>  
> Empty sections are not displayed in the Galaxy tool panel by design.  
> However, can you clarify the behavior when installing a tool shed repository? 
>  Are you saying that empty sections cannot be selected for containing the 
> tool shed repository tools because they are not displayed in the radio button 
> selection list during installation time?  If this is the case, then I'll take 
> a look at this.
>  
> Thanks!
>  
> Greg
>  
> On Feb 6, 2012, at 3:29 AM, Bossers, Alex wrote:
> 
> 
> PS: when I make the section empty again in the original tool_conf.xml it 
> doesn’t show up anymore in that section. :-(
> Actually the complete section is again invisible.
>  
> Van: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex
> Verzonden: maandag 6 februari 2012 8:45
> Aan: 'Greg Von Kuster'; Ira Cooke
> CC: galaxy-dev@lists.bx.psu.edu Dev
> Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
>  
> Hi Greg,
>  
> Ok I pulled the latest changeset and updated the database. No probs.
> Now I am able to get tools from the galaxy main toolshed. Tested the 
> table2html tool to be sure about no additional dependencies. It came up 
> nicely with the section list I can install a tool to; but...
> I created an EMPTY section in the tool_conf.xml menu where I want the 
> toolshed tools to go to at the moment. To keep it maintainable for now at 
> testing. But It does not show up in the bullet list of sections to install to 
> (as these sections also do not show up in the menu itself until they cotain a 
> valid tool xml). Other custom sections are there.
> Part of the tool_conf.xml
>   </section>
> <label text="External tools" id="externaltools" />
>   <section name="ToolShed auto tools" id="toolshedtools">
>   </section>
>  
> I added an empty <tool file=”” /> line in the section and still not there. 
> Adding a valid tool lets it show up in the bullit list as it now also shows 
> up in the left panel.. (as expected).
> Another test on the EMPTY section when I tried adding the tool providing THE 
> SAME section name as custom in the field as a new tool panel section... it 
> just adds it to the end of the section lists in the left. But it does work.
> It also remains working when I enable my own section menu again by adding 
> another tool to the xml first. The section with the same name shows up on two 
> places in the section list when adding tools from toolshed (as expected). 
> Probably due to the different section id. There might be a possible problem 
> when the id turns out the same as an already used one?
>  
> I manually altered the shed_tool_conf.xml to match my section name and id and 
> everything is ok.
>  
> Maybe something to look into? Just a minor issue I think.
>  
> Keep up the good work!
> Alex
>  
>  
>  
> Van: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Greg Von Kuster
> Verzonden: vrijdag 3 februari 2012 22:16
> Aan: Ira Cooke
> CC: galaxy-dev@lists.bx.psu.edu Dev
> Onderwerp: Re: [galaxy-dev] Problem fetching updates to toolshed tool
>  
> Things should be working in change set 6667:86d9c5ddbafc, which is now 
> available from the Galaxy central repository.  Please let me know if you bump 
> into any problems.
> 
> To use the latest features related to tool versioning, update your local tool 
> shed as well as your local Galaxy instance ( both require updating the 
> database schema ).  In your local tool shed, reset all metadata for each 
> repository using the Repository Actions pop-up for each repository.  Since 
> you already have repositories in your tool shed, you'll need to do this once 
> for each existing repository.  Any updates to the repository will 
> automatically do this.  New repositories created from here on will handle 
> this automatically as well.
> 
> 
> 
> Then, in your local Galaxy instance, set tool versions for each installed 
> tool shed repository using the repository's pop-up.
> 
> 
> 
> 
> 
> 
> On Feb 3, 2012, at 11:07 AM, Greg Von Kuster wrote:
> 
> > Hello Ira,
> > 
> > Thanks for reporting this - there are several similar issues that I've 
> > corrected in my next change set, which will be available today.  This 
> > change set will introduce tool versioning for Galaxy tools, whether they 
> > are installed from a tool shed, or are available with the distribution.  
> > This will affect the tool shed as well as repositories installed from tool 
> > sheds that contain tools.  This versioning feature will provide a chain of 
> > ancestor tool versions and descendant tool versions for any tool instance.  
> > 
> > It would be great if you and others that have set up local Galaxy tool 
> > sheds can test this out.  I will get fixes for issues (if any exist) as 
> > fast as possible.  My hope is that this will be the last major feature 
> > introduced until we get everything stabilized a bit more between the tool 
> > shed and Galaxy.
> > 
> > Thanks!
> > 
> > Greg Von Kuster
> > 
> > 
> > On Feb 2, 2012, at 8:40 PM, Ira Cooke wrote:
> > 
> >> Hi, 
> >> 
> >> We've been running into an issue when attempting to create a new toolshed 
> >> tool.  We have the toolshed and the main galaxy web app setup and running, 
> >> but updating our tool to the latest version always fails.
> >> 
> >> When clicking "Get updates" on our installed tool we find that the initial 
> >> request is sent fine to the community application, but the reply is 
> >> missing a slash after the galaxy url.  This causes the request to fail.
> >> 
> >> Our solution to this problem was to modify 
> >> lib/galaxy/webapps/community/controllers/repository.py on line 795 to 
> >> include a slash after the galaxy url.  
> >> 
> >> After we did this though we encountered another problem .. this time in 
> >> lib/galaxy/web/controllers/admin_toolshed.py .  In this case there is a 
> >> named parameter to a method but the name of the parameter does not match 
> >> the method definition.  The problem was on 688 where "name = name" should 
> >> read "repository_name=name". 
> >> 
> >> After making these changes the get updates function seems to work fine. 
> >> 
> >> Hope this helps.
> >> Ira
> >> 
> >> 
> >> 
> >> ___________________________________________________________
> >> 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/
> > 
> > Greg Von Kuster
> > Galaxy Development Team
> > g...@bx.psu.edu
> > 
> > 
> > 
> > 
> > ___________________________________________________________
> > 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/
> 
> Greg Von Kuster
> Galaxy Development Team
> g...@bx.psu.edu
> 
> 
> 
> ___________________________________________________________
> 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/
>  

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