I would not advise doing this. Based on your environment, I recommend that you do not attempt to install tools from the tool shed as doing so may pose problems for the same tools that you have altered in your environment and that you do not want to get "out of sync". On Jul 11, 2012, at 4:09 PM, Anthonius deBoer wrote:
If I drop the following two tables, would those be reconstructed again correctly if I had the XML files in order?
tool_version_association and tool_version
Thanks
Thon
On Jul 11, 2012, at 12:29 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Thon,
What revision of Galaxy are you running? Have you made multiple attempts at the migration? Are you running a postgres database? How many records do you have in your tool_dependency table in your database, and what is the status of each record? Have you made any changes to the Galaxy code base in your environment? Any additional information that you can send will help track down the problem in your environment.
Thanks!
Greg Von Kuster
On Jul 11, 2012, at 2:46 PM, Anthonius deBoer wrote:
I'm getting this error when I try to run the tool migration:
sh ./scripts/migrate_tools/0003_tools.sh install_dependencies No handlers could be found for logger "docutils" Repositories will be installed into configured tool_path location ../shed_tools Adding new row (or updating an existing row) for repository 'freebayes' in the tool_shed_repository table. Traceback (most recent call last): File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module> app = MigrateToolsApplication( sys.argv[ 1 ] ) File "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/migrate/common.py", line 150, in __init__ install_dependencies=install_dependencies ) File "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/install_manager.py", line 37, in __init__ self.install_repository( repository_elem, install_dependencies ) File "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/install_manager.py", line 258, in install_repository install_dependencies=install_dependencies ) File "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/install_manager.py", line 174, in handle_repository_contents tool_dependencies=tool_dependencies ) File "/home/tdeboer/code/galaxy-copy/lib/galaxy/util/shed_util.py", line 1231, in handle_tool_dependencies tool_dependency = install_package( app, elem, tool_shed_repository, tool_dependencies=tool_dependencies ) File "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/tool_dependencies/install_util.py", line 52, in install_package install_dir = get_tool_dependency_install_dir( app, tool_shed_repository, package_name, package_version ) File "/home/tdeboer/code/galaxy-copy/lib/galaxy/tool_shed/tool_dependencies/install_util.py", line 42, in get_tool_dependency_install_dir repository.installed_changeset_revision ) ) File "/home/tdeboer/code/galaxy_env/lib/python2.6/posixpath.py", line 67, in join elif path == '' or path.endswith('/'): AttributeError: 'NoneType' object has no attribute 'endswith'
Any ideas?
Thanks
Thon ___________________________________________________________ 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: