Hello Birgit,

It looks like you are attempting to install from the test Galaxy tool shed, which tracks fairly closely to the Galaxy central repository on bitbucket. What changeset revision of Galaxy are you running? It will always speed up our handling of issues like this if you include this information in your initial emails in the future.

The main Galaxy tool shed now track the Galaxy dist repository on bitbucket.

Thanks,

Greg Von Kuster

On Sep 10, 2012, at 3:44 PM, Birgit Crain wrote:

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%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 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.com

The contents of this e-mail and any attachments are confidential and only for use by the intended recipient. Any unauthorized use, distribution or copying of this message is strictly prohibited. If you are not the intended recipient please inform the sender immediately by reply e-mail and delete this message from your system. Thank you for your co-operation. <cgatools.tar.gz>___________________________________________________________ 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:

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Hello Birgit,

I've committed a fix for this issue in change set revision 7668:802413bc137b, which is currently running on the test tool shed and is currently available only in the Galaxy central repository. This fix will be include in the ext Galaxy distribution scheduled for the end of next week. You'll have to pull from the Galaxy central repo if you want to use the fix before the next release.

Sorry for the inconvenience on this,

Greg Von Kuster

On Sep 10, 2012, at 4:30 PM, Birgit Crain wrote:

I downloaded the latest galaxy-dist this morning and I used the test toolshed to test my repository first before I upload it to the main toolshed. Thanks

Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete Genomics, Inc. (650) 428-6023 office | (408) 605-3938 mobile bcrain@completegenomics.com

From: Greg Von Kuster greg@bx.psu.edu Date: Monday, September 10, 2012 1:06 PM To: Birgit Crain bcrain@completegenomics.com Cc: "galaxy-dev@lists.bx.psu.edu" galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool_data_table.xml and *.loc not installed with repository

Hello Birgit,

It looks like you are attempting to install from the test Galaxy tool shed, which tracks fairly closely to the Galaxy central repository on bitbucket. What changeset revision of Galaxy are you running? It will always speed up our handling of issues like this if you include this information in your initial emails in the future.

The main Galaxy tool shed now track the Galaxy dist repository on bitbucket.

Thanks,

Greg Von Kuster

On Sep 10, 2012, at 3:44 PM, Birgit Crain wrote:

...

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%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 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.com

The contents of this e-mail and any attachments are confidential and only for use by the intended recipient. Any unauthorized use, distribution or copying of this message is strictly prohibited. If you are not the intended recipient please inform the sender immediately by reply e-mail and delete this message from your system. Thank you for your co-operation. <cgatools.tar.gz>___________________________________________________________ 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:

http://lists.bx.psu.edu/

The contents of this e-mail and any attachments are confidential and only for use by the intended recipient. Any unauthorized use, distribution or copying of this message is strictly prohibited. If you are not the intended recipient please inform the sender immediately by reply e-mail and delete this message from your system. Thank you for your co-operation.