On Thu, Sep 2, 2010 at 12:35 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Peter
I've just started looking at installing a local copy of Galaxy, and have registered with the mailing list.
First one quick question - is there an easy way to search the Galaxy wiki (or documentation in general)? Perhaps my questions are already discussed if I knew where to look...
Have a look at
http://bitbucket.org/galaxy/galaxy-central/wiki/SiteMap
and
Helpful, but not quite what I was looking for. Maybe searching the wiki pages for a project is a missing feature in bitbucket?
I understand that to install Galaxy locally we just clone the mercurial repository (either galaxy-central or galaxy-dist) and then use hg to periodically update this to the latest code. i.e. There are no formal releases with a version number that come as a tar ball or similar.
not really a version number, but I recommend to follow the "News Briefs"
http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBriefs
That's useful. Does this also get sent out by email, or on a news server with RSS/Atom feeds? I don't want to have to manually check the wiki every month.
Naturally, once I have a copy of Galaxy, I will be making some changes to it - in particular configuration changes, for example to use PostgreSQL.
Is the the workflow described here the recommend approach?
http://bytebucket.org/galaxy/galaxy-central/wiki/DevConf2010/galaxy_devconf_... (I found this presentation via a Google search)
Have a look at:
http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer
I've seen that and will be working my way though it in detail. However, this doesn't mention using hg to update an existing installation, specifically how to handle merging the upstream changes with any local changes.
If I understand it, the idea is that we rename tool_conf.xml.sample to tool_conf.xml (and remove it from the .hgignore file) so that any changes made to the sample configuration will be merged into our local configuration?
Alternatively, we could just take a copy and leave tool_conf.xml in the ignore file. We would then have to manually apply any changes made to the tool_conf.xml.sample on a case by case basis.
Also do you recommend I make my own changes on a branch?
Depends on how much do you want to change?
For us, adding our own tool is the big thing about Galaxy and we are pretty happy with the default Galaxy distro. Of course we have a few customizations, but they are added very quickly to a new 'release' by hand.
Could you clarify how you update your Galaxy install via hg, specifically regarding preserving local configuration changes and extra tools?
I expect our changes to be just to configuration files, and the addition of some new in-house local tools/workflows. It would seem sensible to track changes to any local tools (e.g. the XML files defining how Galaxy calls them) within the same hg repository. Given I don't plan to make any changes to Galaxy itself, this sort of thing shouldn't cause much trouble for hg merges (I hope).
Thanks,
Peter