Hi John,

Thanks for the note. Please see inline.

On Fri, Mar 7, 2014 at 7:18 PM, John Chilton <jmchil...@gmail.com> wrote:

> Hmm... I am not certain but it sounds like the migration script ripped
> something out of your Galaxy tool panel that you did not want it to? This
> is unfortunate - but I don't think it would happen again now that the
> migration process is complete. Some future update to Galaxy may include
> additional migrations scripts but now that macs is out it won't ever be
> migrated again.  imagine you can just update your tool_conf.xml file to
> point to your existing macs wrapper you set up manually and you can either
> leave the devteam version of macs in place or uninstall it if you prefer
> your own. Is it not this easy?

Yes that's what I thought, but I was worrying that if I remove devteam
version of macs from the migrated_tool.conf, I might break something
potentially useful for galaxy. Mainly, I try not to manually change things
since that would not be maintainable over time. That's why I was asking how
to handle this properly. It's great to have your confirmation that it works
this way. :-)

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