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Not a problem Peter, it's a somewhat subtle bug to have, and there isn't a lot of documentation on the wiki about writing new datatypes (though I plan to fix that soon).
That particular error message could stand to be a bit more explicit. (e.g., "Did you forget to add import mylib to registry.py?").
Also, thanks for sharing the blog post. Since we develop all of our tools internally, I may adapt and publish your post with similar instructions for jenkins, if that's all right by you.
Cheers, Eric
On 07/17/2014 11:46 AM, Peter Cock wrote:
On Thu, Jul 17, 2014 at 4:31 PM, Eric Rasche rasche.eric@yandex.ru wrote:
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For those reading this thread from the future, there's a secret to adding completely new datatypes locally (and not through a toolshed).
You have to manually edit lib/galaxy/datatypes/registry.py and import the module you've written at the top of the file.
For instance, if you add a new "gbk.py" datatype, you'll need to add "import gbk" to the top of registry.py. This will cause your errors to go away and your datatype to be loaded on startup.
Thanks to John Chilton for answering this on IRC.
Cheers, Eric
Indeed - sorry I hadn't spotted that complication.
The README files for these datatype extensions may help:
https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatype... https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes
I have to do this manually with some sed magic in my TravisCI automated set setup, see:
http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-...
Peter