In addition to cloning, you can also download the tarball for each tool just like you used to - see the Repository Options popup menu for each repo.
On Jun 9, 2011, at 2:55 PM, Peter Cock wrote: > 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. > > Peter > > ___________________________________________________________ > 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: > > http://lists.bx.psu.edu/ > Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___________________________________________________________ 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: http://lists.bx.psu.edu/