Manually installing rsem_datatypes package from toolshed
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
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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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
___________________________________________________________ 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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Ryan G