Proprietary datatypes are loaded before datatypes in the distribution as of
change set revision 6693:865d998a693d, which is available in our central repo.
Proprietary datatypes contained in installed repositories are loaded in order
of oldest installation first, followed by next olderst
To clarify, proprietary datatypes currently being loaded will be ignored if
they conflict with a proprietary datatypes that was already loaded. Only
datatypes defined in the datatypes_conf.xml file will take precedence, and
override conflicts.
On Feb 8, 2012, at 11:34 AM, Greg Von Kuster
In revision 6695:c06d7cef9125 I simplified the precedence rules. A datatypes
currently being loaded will always replace a conflicting datatype that was
previously loaded. This same behavior applies to datatype sniffers (sniffers
loaded later will replace sniffers loaded previously), but will
Hello Ira,
Very sorry for the back-and-forth on this. The behavior you encountered was
accurate - the environment in which I was testing was not pristine. I have
committed a fix for this issue in revision b4ba8b20d78d, which is now available
from our central repo.
I started looking at
Hi Greg,
Thanks for that fix ... I'll check it out.
I think the issue of sniff order is a pretty important one for shed tools that
require proprietary datatypes. The problem is that galaxy's default sniffers
include some extremely generic sniffers (eg text,xml) which will catch pretty
much
Ira,
Thanks for the feedback - I'll come up with something that allows for
proprietary sniffers to be loaded first and let you know when it's available.
It shouldn't take me too long. I will probably continue to keep the rule of
ignoring conflicts in proprietary datatypes, so sniffers for
Hi Greg,
Thanks .. that sounds like a good solution. I'll be happy to test it when its
ready.
Ira
On 08/02/2012, at 10:22 AM, Greg Von Kuster wrote:
Ira,
Thanks for the feedback - I'll come up with something that allows for
proprietary sniffers to be loaded first and let you know when
Hello Ira,
I believe proprietary datatype sniffers included in tool shed repositories are
loading as expected - at least I cannot reproduce the behavior you are seeing.
The datatypes_conf.xml file included in the latest revision of the gmap
repository on the main Galaxy tool shed looks like
Hello Ira,
I will fix the sniff problem with proprietary data types included in tool sheds
- I should be able to have this fixed within the next day or two. With regard
to the upload tool respecting these sniffers, I've already designed this tool
as well as the metadata setting components to
