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_reposito... 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 <clements@galaxyproject.org> wrote:

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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 <wuxbl@mit.edu> wrote:

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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 <greg@bx.psu.edu> wrote:

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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:

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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 <clements@galaxyproject.org> wrote:

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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/