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&changeset_revisions=982e19c29ec0 HTTP/1.1" 200 - "http://testtoolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=96d1ef4698eaa22d&changeset_revision=982e19c29ec0&webapp=galaxy" "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=http://testtoolshed.g2.bx.psu.edu/&repository_ids=96d1ef4698eaa22d&changeset_revisions=982e19c29ec0" "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=http://testtoolshed.g2.bx.psu.edu/&repository_ids=96d1ef4698eaa22d&changeset_revisions=982e19c29ec0" "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_repository_ids=f2db41e1fa331b3e&reinstalling=False&encoded_kwd=80e690a1cf32f1294e27873f210c5344dc427413%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" "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

 
 
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