Simon, What is the advantage of putting that XML definition in the tool shed? It is not 100% true because of prior_install_required dependencies, but for the most part sourcing/load the environment for tools is a Galaxy problem, not so much a tool shed one. What if we did this instead?
Add an option to Galaxy's universe_wsgi.ini with the following default: tool_dependency_resolution_order = gx_package_manual, gx_package_toolshed Which essentially implements my idea above, with James' additional configuration. But which can be overridden as: tool_dependency_resolution_order = plugin_module, gx_package_manual, gx_package_toolshed If set this way then placing <requirement package="0.5.9">bwa</requirement> in a tool will result in the module bwa/0.5.9 being loaded if it is 'avail'able, else it will check for a manually installed env.sh (which is where MSI is currently putting its module loads), and else it will fallback to source the tool shed installed dependency. I feel like this will give you everything you want without any extra XML or configuration. Let me know if I am wrong. -John On Thu, Sep 26, 2013 at 11:39 PM, Guest, Simon <simon.gu...@agresearch.co.nz> wrote: > At Thu, 26 Sep 2013 22:03:09 -0400, > Greg Von Kuster wrote: >> >> Hi John, >> >> On Sep 26, 2013, at 9:15 PM, John Chilton <chil...@msi.umn.edu> wrote: >> >> > I was not even thinking we needed to modify the tool shed to implement >> > this. I was hoping (?) you could just modify: >> >> Nothing in the Tool Shed itself would be affected or require modification >> for this new feature as this is completely on the Galaxy side. >> >> > >> > lib/galaxy/tools/deps/__init__.py >> > >> > to implement this. If some tool contains the tag >> > >> > <requirement type="package" version="1.7.1">numpy</requirement> >> > >> > then if there is a manually installed tool_dependency in >> > `tool_dependency_dir/numpy/1.7.1/env.sh` that would take precedence >> > over the tool shed installed version (would that be something like >> > `tool_dependency_dir/numpy/1.7.1/owner/name/changeset/env.sh`)? Let me >> > know if this is way off base. >> >> This is a possibility perhaps, but there seems to be a potential weakness in >> that it doesn't require the Tool Dependency object to exist since the tool >> will function without a installed dependency from the Tool Shed. Or, if the >> installed depndency s required, then it is meaningless because it won't be >> used. If the former case, then the tool dependency cannot be shared via the >> Tool Shed's dependency mechanism because none of the relationships will be >> defined since nothing is installed. Wouldn't it be better to allow the >> Galaxy admin to point the ToolDependency object to a specified binary on >> disk? In this way, all relationships defined by Tool Shed installations >> will work as expected, with all contained tools with that dependency point >> to that same shared location on disk. > > Hi Greg, John, > > What you are discussing is pretty close to what I am after, and what I > am prepared to spend some time working on, if that can help. This is > what I have posted about a couple of times previously. The option to > use a pre-installed package rather than a Galaxy installed one I think > would be very useful in general. I think it can be done in a way that > doesn't break the tool dependency model. > > I envisage providing access to existing programs on disk by loading > the relevant environment module. Platforms will differ greatly on > where they have programs installed (usr/local/bwa-0.5.9, > /usr/libexec/bwa-0.5.9, etc.). However, we could arrange to have a > conventionally named environment module available, so Galaxy just has > to be told somehow to do a module load bwa/0.5.9, say, prior to > trying to run that tool, which will then be found on the PATH. > > Hooking this in without killing the dependency on named and versioned > toolshed repos could work like this. In parallel with the repo sets > named, e.g. package_bwa_0_5_9, which download and build the package, > we have a set named like native_package_bwa_0_5_9. This could have a > tool_dependencies.xml file like this: > > <?xml version="1.0"?> > <tool_dependency> > <native_package name="bwa" version="0.5.9"> > <actions> > <action type="load_module"> > <module name="bwa" version="0.5.9"</module> > </action> > </actions> > <readme> > Uses native BWA via environment module bwa/0.5.9 > </readme> > </native_package> > </tool_dependency> > > What this does is ensure that any repo which requires version 0.5.9 of > bwa can have this dependency resolved by either package_bwa_0_5_9, or > native_package_bwa_0_5_9. > > I envisage a Galaxy configuration setting that enables native package > and/or Galaxy package dependency resolution, and which one should be > preferred. Of course, if one of these has been manually installed, it > will be used as is. > > I would really like to be able to install tools from the toolshed, and > have them resolve their dependencies automatically using my > preinstalled application suite. I see that would also meet the needs > being discussed here. > > How does that sound? > > cheers, > Simon > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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