Hi
I got a problem with the tool_data_table.xml and tool-data/*.loc files when testing the download of my repository.
My repository contains a *.loc.sample file and a tool_data_table_conf.xml.sample (they were unchanged from my last upload to the repository). When installing the repository I get the following messages:
172.22.128.28 - - [10/Sep/2012:11:46:16 -0700] "GET /admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftesttoolshed.g2.bx.psu.edu%2F HTTP/1.1" 302 - "http://lx-galaxy-1:8080/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:15.0) Gecko/20100101 Firefox/15.0.1" 172.22.128.28 - - [10/Sep/2012:11:46:39 -0700] "GET /admin_toolshed/prepare_for_install?tool_shed_url=http://testtoolshed.g2.bx.psu.edu/&repository_ids=96d1ef4698eaa22d&c... HTTP/1.1" 200 - "http://testtoolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repo..." "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:15.0) Gecko/20100101 Firefox/15.0.1" Adding new row (or updating an existing row) for repository 'testing_cgatools' in the tool_shed_repository table. galaxy.web.controllers.admin_toolshed DEBUG 2012-09-10 11:47:27,751 Appending to tool panel section: CG tools 172.22.128.28 - - [10/Sep/2012:11:47:27 -0700] "POST /admin_toolshed/prepare_for_install?encoded_repo_info_dicts=606805d7b3160cf8502df2b105df5510f61a250c%3A7b2274657374696e675f636761746f6f6c73223a205b22746869732069732061207465737420222c2022687474703a2f2f74657374746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f62637261696e2d636f6d706c65746567656e6f6d6963732f74657374696e675f636761746f6f6c73222c2022393832653139633239656330222c20223233222c202262637261696e2d636f6d706c65746567656e6f6d696373222c206e756c6c5d7d&includes_tools=True&tool_shed_url=http%3A%2F%2Ftesttoolshed.g2.bx.psu.edu%2F&includes_tool_dependencies=False HTTP/1.1" 302 - "http://lx-galaxy-1:8080/admin_toolshed/prepare_for_install?tool_shed_url=htt..." "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:15.0) Gecko/20100101 Firefox/15.0.1" 172.22.128.28 - - [10/Sep/2012:11:47:27 -0700] "GET /admin_toolshed/initiate_repository_installation?shed_repository_ids=f2db41e1fa331b3e&reinstalling=False&encoded_kwd=80e690a1cf32f1294e27873f210c5344dc427413%3A7b22737461747573223a2022646f6e65222c2022746f6f6c5f70616e656c5f73656374696f6e5f6b6579223a202273656374696f6e5f63675f746f6f6c73222c2022746f6f6c5f736865645f7265706f7369746f72795f696473223a205b2266326462343165316661333331623365225d2c2022736865645f746f6f6c5f636f6e66223a20222e2f736865645f746f6f6c5f636f6e662e786d6c222c2022746f6f6c5f70617468223a20222e2e2f736865645f746f6f6c73222c20227265706f5f696e666f5f6469637473223a205b22363036383035643762333136306366383530326466326231303564663535313066363161323530633a376232323734363537333734363936653637356636333637363137343666366636633733323233613230356232323734363836393733323036393733323036313230373436353733373432303232326332303232363837343734373033613266326637343635373337343734366636663663373336383635363432653637333232653632373832653730373337353265363536343735326637323635373036663733326636323633373236313639366532643633366636643730366336353734363536373635366536663664363936333733326637343635373337343639366536373566363336373631373436663666366337333232326332303232333933383332363533313339363333323339363536333330323232633230323233323333323232633230323236323633373236313639366532643633366636643730366336353734363536373635366536663664363936333733323232633230366537353663366335643764225d2c2022696e7374616c6c5f746f6f6c5f646570656e64656e63696573223a2066616c73652c2022696e636c756465735f746f6f6c73223a20747275652c2022746f6f6c5f736865645f75726c223a2022687474703a2f2f74657374746f6f6c736865642e67322e62782e7073752e6564752f222c20226d657373616765223a2022222c2022696e636c756465735f746f6f6c5f646570656e64656e63696573223a2066616c73657d HTTP/1.1" 200 - "http://lx-galaxy-1:8080/admin_toolshed/prepare_for_install?tool_shed_url=htt..." "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:15.0) Gecko/20100101 Firefox/15.0.1" 172.22.128.28 - - [10/Sep/2012:11:47:31 -0700] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://lx-galaxy-1:8080/admin_toolshed/initiate_repository_installation?shed..." "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:15.0) Gecko/20100101 Firefox/15.0.1" galaxy.tools.data WARNING 2012-09-10 11:47:32,181 Cannot find index file 'tool-data/cg_crr_files.loc' for tool data table 'cg_crr_files' galaxy.tools.data DEBUG 2012-09-10 11:47:32,181 Loaded tool data table 'cg_crr_files'
The 'cg_crr_files.loc' is not created and the tool_data_table.xml does not get updated with the information from the tool_data_table.xml.sample file in the repository. Is this a bug or has something changed that I'm not aware of with regards to the tool-data files and tool_data_table.xml?
Thanks
Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete Genomics, Inc. (650) 428-6023 office | (408) 605-3938 mobile bcrain@completegenomics.commailto:bcrain@completegenomics.com
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