Hello Xuebing,

Your updates that will be available for an installed repository are restricted 
to the version that is installed where the version is defined by the change set 
revision number.  This enables different versions of tools in the repository to 
always be accessible and installable.

The following explanation is taken from the tool shed wiki.

http://wiki.g2.bx.psu.edu/Tool%20Shed#Getting_updates_for_tool_shed_repositories_installed_in_a_local_Galaxy_instance

A very important point to convey here is that updates retrieved from the 
relevant Galaxy tool shed will be restricted to the latest change set that 
includes those versions of tools that are currently in your installed tool shed 
repository.  Remember that the tool shed repository revision values are a 
number followed by a : and an alpha-numeric string (e.g., 6:98d05121d41e).  
Let's assume that at some point you installed revision 0:sdj45ger5fr4 of a tool 
shed repository into your local Galaxy instance.  Then at some later point the 
related repository in the Galaxy tool shed was updated with revision 
1:si88rhjk8hfh.  Then even later the same repository in the Galaxy tool shed 
was updated to a new revision number, say 2:srjls89ojf8e.  Let's assume that 
this latest version resulted in a Revision select list for the repository in 
the Galaxy tool shed because the version of one or more tools within the 
repository changed.  If you updated your locally installed tool shed repository 
after these changes to the repository within the Galaxy tool shed were made, 
your local repository would be updated to revision 1:si88rhjk8hfh, but would 
not be updated to include the change in revision 2:srjls89ojf8e.  Since 
revision 2:srjls89ojf8e of the repository within the Galaxy tool shed includes 
tools that have different versions, you have to install that revision into your 
local Galaxy instance as a separate tool shed repository installation if you 
want to use the new versions of the tools.


On Mar 16, 2012, at 3:52 PM, Xuebing Wu wrote:

> Hi Dave,
> 
> I'm not sure if this is the right way to ask questions about tool
> shed: I'm having trouble updating my tools installed in a local
> instance. I deleted old xml files and uploaded a new one. I can see
> revision number changes in toolshed website, but when I tried to
> manually update tools by clicking "Get Updates" item in "Repository
> Actions", I got message saying that there is no updates available.
> 
> best,
> Xuebing
> 
> On Tue, Mar 13, 2012 at 7:01 PM, Dave Clements
> <cleme...@galaxyproject.org> wrote:
>> Hi Xuebing,
>> 
>> if you are planning to make these available in small pieces, then I won't
>> Tweet sharplabtool (unless you tell me to!).
>> 
>> However, I will Tweet the smaller repositories, if and when they show up.
>> 
>> Thanks for sharing this with the community,
>> 
>> Dave C
>> 
>> 
>> 
>> On Tue, Mar 13, 2012 at 3:34 PM, Xuebing Wu <wu...@mit.edu> wrote:
>>> 
>>> I see. It's a set of tools we have on our local galaxy server. So it's
>>> pretty heterogeneous, including interval manipulation, meta-gene
>>> analysis, sequence and motif analysis, and some others. I don't have a
>>> good description for them. I'm planning to separately them anyway.
>>> 
>>> best,
>>> Xuebing
>>> 
>>> On Tue, Mar 13, 2012 at 6:26 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>>>> Xuebing, it's fine to have many tools in the same repository, so please
>>>> don't feel you have to separate them into multiple repositories unless it 
>>>> is
>>>> something you were planning anyway.  Dave is just wondering if you have a
>>>> good description for the set of tools you have made available.
>>>> 
>>>> Thanks!
>>>> 
>>>> On Mar 13, 2012, at 5:58 PM, Xuebing Wu wrote:
>>>> 
>>>>> Sorry about this. I'm just testing. May be I should try the test
>>>>> website first. I'll remove them and then create separate repositories.
>>>>> 
>>>>> best,
>>>>> Xuebing
>>>>> 
>>>>> On Tue, Mar 13, 2012 at 5:22 PM, Dave Clements
>>>>> <cleme...@galaxyproject.org> wrote:
>>>>>> Dear Xuebing,
>>>>>> 
>>>>>> Several days ago you created the new "sharplabtool" in the Galaxy Tool
>>>>>> Shed.  Normally, I tweet newly deposited tools, but I am not sure how
>>>>>> to
>>>>>> summarize this repository.  It is enormous and includes many tools
>>>>>> that
>>>>>> would be generally useful at many Galaxy installations.  Is there a
>>>>>> more
>>>>>> informative summary than "sharplabtool" that I could use in the Tweet?
>>>>>>  I
>>>>>> can also make something up.
>>>>>> 
>>>>>> Thanks,
>>>>>> 
>>>>>> Dave C
>>>>>> 
>>>>>> --
>>>>>> http://galaxyproject.org/GCC2012
>>>>>> http://galaxyproject.org/
>>>>>> http://getgalaxy.org/
>>>>>> http://usegalaxy.org/
>>>>>> http://galaxyproject.org/wiki/
>>>>>> 
>>>>> 
>>>> 
>> 
>> 
>> 
>> 
>> --
>> http://galaxyproject.org/GCC2012
>> http://galaxyproject.org/
>> http://getgalaxy.org/
>> http://usegalaxy.org/
>> http://galaxyproject.org/wiki/
>> 
> 

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