On Dec 10, 2012, at 1:14 PM, greg wrote:

> Thanks, but I think now I'm even more confused :-(

Hmm...sorry.  I highly advise you to read the tool shed wiki as it will clear 
up a lot of your confusion.

> It seems like a whole lot of the tools that are listed on the left
> panel after installing galaxy aren't actually installed.

I'm not sure to what tools you are referring here, but some Galaxy tools 
consist of 2 components ( a UI based on Cheetah, and a script that has no 
requirements ) while others have a 3rd component ( a 3rd-party dependency ).  
When you clone the Galaxy distribution, those tools that require dependencies 
must have those dependencies manually installed and defined on a path in such a 
way that the Galaxy user ( the account used to start the Galaxy server ) can 
find them.  This has always been the case, and has nothing to do with the tool 

However, the tool shed improves this process for those repositories that you 
install into your Galaxy instance that include tools and defined dependencies 
for them.

> For example FastQC.  Then I do see FastQC in the tool shed, but it
> seems like when I go to install it, it will create its own entry on
> the left panel and not fix the FastQC tool that's already there.

These are 2 different tools, although they are named similarly.  You'll notice, 
though, that they have different IDs.  So installing a tool from the tool shed 
will not fix or replace an existing tool with the same name in a Galaxy 
instance into which it was installed.

> So if I install everything I can from the tool shed I'll still be left
> with a whole lot of broken tools in the left panel?

Possibly - again, it is the responsibility of the repository owner to ensure 
the tools are functionally correct when installed into Galaxy.  A commission is 
in place to review and approve the contents of repositories on the main Galaxy 
tool shed, but it has not yet undertaken this endeavor.

> (I guess the tool shed is just for new tools, and not to fix the ones
> already listed in Galaxy.  

Any tools included in the Galaxy distribution does not need "fixing".  At most 
they need a dependency to be manually installed.  See the tool dependencies 
page in the Galaxy wiki for details.  It's available here:


> Would it make sense to stop including tool
> links on the left panel that aren't bundled with Galaxy, and then let
> the toolshed add them in?)

Not sure what you mean here.

> -Greg
> On Mon, Dec 10, 2012 at 11:16 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> Hi Greg,
>> In case you haven't found it, the tool shed wiki provides a lot of 
>> information.  It's available at  http://wiki.galaxyproject.org/Tool%20Shed
>> On Dec 10, 2012, at 10:59 AM, greg wrote:
>>> Hi guys,
>>> I have my fresh galaxy install on our cluster and now I'm trying to
>>> figure out which tools are missing and how to install them.
>>> I just came across the toolshed so now I'm really confused.
>>> Question 1:
>>> Can I install EVERY tool I need from the tool shed or are there some
>>> things I need to install manually first like R, Samtools, etc?  How do
>>> I know what to install from where?
>> The intent of the tool shed is to share Galaxy utilities (  tools, exported 
>> workflows, proprietary datatypes, etc) developed by many contributors in the 
>> Galaxy community.  The tool shed provides a very rich set of features that 
>> enhance those provided by Galaxy itself.  In this way it complements galaxy. 
>>  For example, the tool shed provides features that allow tool developers to 
>> include information within their tool shed repository to automatically 
>> install ( and possibly compile ) tool dependencies for tools within the 
>> repository.
>> However, it is up to the repository owner (the community contributor ) to 
>> use tool shed features like this.  So some repositories include tools that 
>> will install dependencies, while others require manual dependency 
>> installation.
>> The core Galaxy development team is in the process of migrating tools from 
>> the Galaxy distribution to the main Galaxy tool shed.  Tools that have been 
>> migrated in this way are all contained in repositories with the owner 
>> "devteam".  If these repositories include tools, then they will have 
>> dependencies defined for them, so the dependencies will be installed along 
>> with the repositories.
>>> Question 2:
>>> Is it preferable to use the toolshed whenever possible, or it is not
>>> fully developed yet?
>> It is preferable to use the tool shed whenever possible, but additional 
>> features will continue to be added.   This does not imply that you have to 
>> wait for additional features before using the tool shed.
>>> Thanks,
>>> Greg
>>> ___________________________________________________________
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>> Greg Von Kuster

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