On Wed, Nov 23, 2016 at 10:49 AM, Peter Briggs
<peter.bri...@manchester.ac.uk> wrote:
> Hello Evan, Hans-Rudolf
> I'm just in the middle of doing a similar migration for our local production
> server, and Hans-Rudolf's advice seems sound to me. Definitely moving the
> core Galaxy server has been relatively straightforward.
> However: for the installed tools, I'm not sure that changing the paths in
> the env.sh files is sufficient - in our installation the absolute paths
> seemed to be baked into a lot of other files under the 'tool_dependencies'
> directory - including things like compiled files (e.g. static and shared
> libraries). So for many of the tools I wouldn't feel confident that they
> would still work after the move.

Yes, I've seen that with various third party tool installations (out side of
Galaxy), so sadly you cannot in general move the files to a different path :(

I don't know if we can do anything about this directly in Galaxy, or even
in BioConda?

> My plan has been to reinstall each of the tools from the toolshed (i.e.
> uninstall via the admin interface then reinstall the same tool repository
> revision(s) using the API), but I don't feel able to recommend this approach
> either as in my testing this has also had problems - ranging from some tool
> revisions no longer being available, through to more serious issues (such as
> tool dependencies which used to work but since become broken). I figured I'd
> just have to knuckle down and work through each problem as I encountered it.

One simple reason for this is stale URLs, where Galaxy's cache can help
but is another step for tool wrapper authors to do when setting up a new
Galaxy dependency: https://github.com/galaxyproject/cargo-port

However, even well intentioned Tool Shed updates could also break things :(

> If anyone else has experiences with these kinds of migrations then I'm also
> very interested to know what worked (and what didn't)!

Sorry - the closest I've been is setting up a new Galaxy server in
parallel with our old server, and manually installing "missing" tools
via the Tool Shed.

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