Yup, that fixed it. Thanks!

On Wed, Jan 21, 2015 at 6:51 PM, John Chilton jmchilton@gmail.com wrote:

I believe this is an ancient bug that I has been fixed in Galaxy's central branch but is not in the latest release:

https://bitbucket.org/galaxy/galaxy-central/commits/1422966f1ca88472b8685015...

The previous workaround for this bug was that one would need to import the datatype at the top of registry.py (import rsem_datatypes) which is another option for addressing this problem instead of applying the patch.

Hope this helps, -John

On Wed, Jan 21, 2015 at 2:16 PM, Ryan G ngsbioinformatics@gmail.com wrote:

...

I'm trying to manually install rsem_datatypes package into my local

Galaxy

...

install. I can't use the Toolshed for various reasons.

Anyway, I downloaded the package using

hg clone https://toolshed.g2.bx.psu.edu/repos/jjohnson/rsem_datatypes

I see two files:

1. datatypes_conf.xml, and
2. rsem.py

I copied the <datatype extension ...> lines into my config/datatypes_conf.xml file. I also copied rsem.py to lib/galaxy/datatypes/.

When I restart Galaxy, it doesn't seem that Galaxy knows how to handle

rsem

...

datatypes, as I get this error:

galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,519 Error importing datatype module galaxy.datatypes.rsem: 'module' object has no attribute 'rsem' Traceback (most recent call last): File "/data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 210, in load_datatypes module = getattr( module, mod ) AttributeError: 'module' object has no attribute 'rsem' galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,519 Error importing datatype module galaxy.datatypes.rsem: 'module' object has no attribute 'rsem' Traceback (most recent call last): File "/data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 210, in load_datatypes module = getattr( module, mod ) AttributeError: 'module' object has no attribute 'rsem' galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,520 Error importing datatype module galaxy.datatypes.rsem: 'module' object has no attribute 'rsem' Traceback (most recent call last): File "/data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 210, in load_datatypes module = getattr( module, mod ) AttributeError: 'module' object has no attribute 'rsem'

I'm obviously missing something but not sure what. I suspect maybe the rsem.py file is not in the right place?

Ryan

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