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