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
> 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.
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Greg Von Kuster
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: