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.

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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to