On Thu, Jun 9, 2011 at 7:15 PM, Assaf Gordon <gor...@cshl.edu> wrote:
> Hi,
> with the new ToolShed inplace, and support for cloning/pulling tools
> directly: What's the recommend way to organize the repositories ?
> For example, I want to use Peter's Venn tool:
> hg clone http://toolshed.g2.bx.psu.edu/repos/peterjc/venn_list
> If I clone, I get the following folder hierarchy:
> venn_list -> tools -> plotting -> xml/py .
> So I can't directly clone into the <galaxy>/tools folder.
> Even if I could (somehow skipping the "venn_list" directory),
> cloning multiple tools would override the ".hg" folder of each other.
> so is it still a manual process of cloning to a temporary directory,
> then manually copy the files to the <galaxy>/tools folder ? or am
> I missing something ?
> being able to automagically "pull -u" tools from the toolshed
> would be really cool.
> thanks,
>  -gordon

Good question Gordon,

Back on the old tar-ball based Tool Shed, the guidelines were
quite loose about directory structures - at least one folder was
recommended though.

I used to do things expecting the user to be able to untar it
in the root Galaxy folder. Consider we might have test files,
configuration files (e.g. a sample loc file), as well as the core
XML file and any associated scripts.

I'm happy to restructure if there are clear guidelines.

In this case, you could probably clone the Venn diagram
tool anywhere, and reference it in tool_conf.xml with an
absolute path (or relative with a few .. entries). This should
be fine in this case as there are no other data files.


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:


Reply via email to