Re: [galaxy-dev] tool_data_table.xml and *.loc not installed with repository
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 > bcr...@completegenomics.com > > > From: Greg Von Kuster > Date: Monday, September 10, 2012 1:06 PM > To: Birgit Crain > Cc: "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%3A7b22737461747573223a2022646f6e65222c2022746f6f6c5f70616e656c5f73656374696f6e5f6b6579223a202273656374696f6e5f63675f746f6f6c73222c2022746f6f6c5f736865645f7265706f7369746f72795f696473223a205b226632646234316531666131623365225d2c2022736865645f746f6f6c5f636f6e66223a20222e2f736865645f746f6f6c5f636f6
Re: [galaxy-dev] tool_data_table.xml and *.loc not installed with repository
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 bcr...@completegenomics.com<mailto:bcr...@completegenomics.com> From: Greg Von Kuster mailto:g...@bx.psu.edu>> Date: Monday, September 10, 2012 1:06 PM To: Birgit Crain mailto:bcr...@completegenomics.com>> Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" mailto: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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
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 - > "
