Hi Geert, please include this at the top: from galaxy.datatypes.binary import Binary Cheers, Bjoern Am 04.08.2014 um 15:02 schrieb Geert Vandeweyer:
Hi all,
I'm trying to create a new binary datatype in galaxy, but I'm running into troubles. The current installer is available at https://testtoolshed.g2.bx.psu.edu/view/geert-vandeweyer/cuffquant_datatype
When I install the repository to a local server, I get the errors below (no module binary). Since I'm new to defining datatypes, any insights on what I'm doing wrong is welcome :-)
Best,
Geert
tool_shed.util.repository_dependency_util DEBUG 2014-08-04 14:39:07,313 Building repository dependency relationships... 127.0.0.1 - - [04/Aug/2014:14:39:03 +0200] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 200 - "http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=https://testtoolshed.g2.bx.psu.edu/&repository_ids=80b80f5c54443265&changeset_revisions=e12a09256097" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/34.0.1847.116 Chrome/34.0.1847.116 Safari/537.36" 127.0.0.1 - - [04/Aug/2014:14:39:10 +0200] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://127.0.0.1:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/34.0.1847.116 Chrome/34.0.1847.116 Safari/537.36" galaxy.datatypes.registry DEBUG 2014-08-04 14:39:11,362 Loading datatypes from /home/gvandeweyer/galaxy-dist/galaxy-dist/database/tmp/tmp-toolshed-acalpdGx1tEP
galaxy.datatypes.registry DEBUG 2014-08-04 14:39:11,363 Exception importing proprietary code file /home/gvandeweyer/galaxy-dist/shed_tools/testtoolshed.g2.bx.psu.edu/repos/geert-vandeweyer/cuffquant_datatype/f7801f8191e0/cuffquant_datatype/binary: No module named binary galaxy.datatypes.registry ERROR 2014-08-04 14:39:11,363 Error importing datatype module galaxy.datatypes.binary: 'module' object has no attribute 'Cuffquant' Traceback (most recent call last): File "/home/gvandeweyer/galaxy-dist/galaxy-dist/lib/galaxy/datatypes/registry.py", line 207, in load_datatypes datatype_class = getattr( module, datatype_class_name ) AttributeError: 'module' object has no attribute 'Cuffquant' galaxy.datatypes.registry ERROR 2014-08-04 14:39:11,364 Error calling method Cuffquant from class <module 'galaxy.datatypes.binary' from '/home/gvandeweyer/galaxy-dist/galaxy-dist/lib/galaxy/datatypes/binary.pyc'>: 'module' object has no attribute 'Cuffquant' Traceback (most recent call last): File "/home/gvandeweyer/galaxy-dist/galaxy-dist/lib/galaxy/datatypes/registry.py", line 349, in load_datatype_sniffers aclass = getattr( module, datatype_class_name )() AttributeError: 'module' object has no attribute 'Cuffquant'