Yup, that fixed it. Thanks! On Wed, Jan 21, 2015 at 6:51 PM, John Chilton <jmchil...@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/1422966f1ca88472b8685015f5a8cdd3dd0f1db9 > > 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 <ngsbioinformat...@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 > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ >
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