Hi, I'm having trouble with some of my tools not appearing in the Analyze Data menu. I've successfully installed the tools via the manage installed tool shed repositories(so they are installed to disk). I have tried uninstalling and installing again. The tool installs but does not appear in the menu. Other tools install the menu updates just fine. This is probably due to me corrupting the misbehaving tools installation somehow. I'm guessing that I need to uninstall the tool and wipe some postgres entries. My shed tool path: <toolbox tool_path="../shed_tools"> My current version: parent: 12441:dc067a95261d Added tag release_2014.02.10 for changeset 5e605ed6069f branch: stable Could someone point me in the right direction? Thanks, -Sheldon Sheldon Briand NRC Research Computing Support Analyst Research Computing Support / Soutien Informartique a la Recherche Operations, Science Portfolio / Operations, Portefeuil des sciences SSC-NRC / SPC-CNRC Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford Halifax, NS B3H 3Z1 902 426-1677 sheldon.briand@ssc-spc.gc.ca
Hi, I've been poking around a bit more. It looks as though galaxy isn't actually downloading and installing the tools. The tool status changes to installed in the web interface and postgres but the tool is not present on disk. The log below shows no download and make of the tool and dependancies. Hopefully the log gives a bit more information. Sorry for the second email. Thanks, -Sheldon tool_shed.util.shed_util_common DEBUG 2014-02-28 09:58:48,567 Updating an existing row for repository 'tophat2' in the tool_shed_repository table, status set to 'New'. tool_shed.util.repository_dependency_util DEBUG 2014-02-28 09:58:48,714 Creating repository dependency objects... tool_shed.util.shed_util_common DEBUG 2014-02-28 09:58:49,255 Updating an existing row for repository 'tophat2' in the tool_shed_repository table, status set to 'New'. tool_shed.util.repository_dependency_util DEBUG 2014-02-28 09:58:49,269 Building repository dependency relationships... 127.0.0.1 - - [28/Feb/2014:09:58:48 -0300] "POST /admin_toolshed/reinstall_repository?id=827fffb0dffdf266 HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/reselect_tool_pa nel_section?sort=name&advanced_search=true&f-deleted=True&async=false&show_item_checkboxes=false&id=827fffb0dffdf266&page=1" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/201 00101 Firefox/24.0" 132.246.247.143 - - [28/Feb/2014:09:58:51 -0300] "GET /api/histories/c24fc4d33a334292/contents HTTP/1.0" 200 - "http://eugene.imb.nrc.ca/" "Mozilla/5.0 (X11; Linux x86_64; rv:2 4.0) Gecko/20100101 Firefox/24.0" 132.246.244.216 - - [28/Feb/2014:09:58:52 -0300] "GET /api/histories/289a2a0291e69024/contents HTTP/1.0" 200 - "http://eugene.imb.nrc.ca/root/index" "Mozilla/4.0 (compatible; M SIE 7.0; Windows NT 6.1; WOW64; Trident/5.0; SLCC2; .NET CLR 2.0.50727; .NET CLR 3.5.30729; .NET CLR 3.0.30729; Media Center PC 6.0; .NET4.0C; .NET4.0E)" galaxy.tools.data WARNING 2014-02-28 09:58:52,416 Cannot find index file './database/tmp/tmp-toolshed-gmfcr_q5JBB/bowtie2_indices.loc' for tool data table 'tophat2_indexes' galaxy.tools.data DEBUG 2014-02-28 09:58:52,416 Loading another instance of data table 'tophat2_indexes', attempting to merge content. 127.0.0.1 - - [28/Feb/2014:09:58:52 -0300] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/reinstall_reposito ry?id=827fffb0dffdf266" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" galaxy.tools.data DEBUG 2014-02-28 09:58:52,611 Loading another instance of data table 'tophat2_indexes', attempting to merge content. galaxy.tools.test INFO 2014-02-28 09:58:52,624 tophat2 - Failed to find case matching value (No) for test parameter specification for conditional readGroup. Remainder of test b ehavior is unspecified. galaxy.tools.test INFO 2014-02-28 09:58:52,636 tophat2 - Failed to find case matching value (No) for test parameter specification for conditional readGroup. Remainder of test b ehavior is unspecified. galaxy.tools.test INFO 2014-02-28 09:58:52,650 tophat2 - Failed to find case matching value (No) for test parameter specification for conditional readGroup. Remainder of test b ehavior is unspecified. galaxy.tools.test INFO 2014-02-28 09:58:52,664 tophat2 - Failed to find case matching value (No) for test parameter specification for conditional readGroup. Remainder of test b ehavior is unspecified. galaxy.tools.data DEBUG 2014-02-28 09:58:53,154 Could not parse existing tool data table config, assume no existing elements: [Errno 2] No such file or directory: u'/software/p ackages/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/tophat2/ffa30bedbee3/tool_data_table_conf.xml' galaxy.tools.data DEBUG 2014-02-28 09:58:53,167 Loading another instance of data table 'tophat2_indexes', attempting to merge content. galaxy.tools DEBUG 2014-02-28 09:58:53,516 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6, version: 0.6 into tool panel. 127.0.0.1 - - [28/Feb/2014:09:58:55 -0300] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/reinstall_reposito ry?id=827fffb0dffdf266" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" tool_shed.util.common_install_util DEBUG 2014-02-28 09:58:57,748 Attempting to install tool dependency package bowtie2 version 2.1.0. tool_shed.util.tool_dependency_util DEBUG 2014-02-28 09:58:58,038 Updating an existing record for version 2.1.0 of tool dependency bowtie2 for revision ffa30bedbee3 of reposito ry tophat2 by updating the status from Uninstalled to Never installed. [localhost] local: touch ./dependancies/bowtie2/2.1.0/devteam/tophat2/ffa30bedbee3/env.sh [localhost] local: echo 'if [ -f /software/packages/galaxy/galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/env.sh ] ; then . /software/package s/galaxy/galaxy-dist/dependancies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/env.sh ; fi' >> ./dependancies/bowtie2/2.1.0/devteam/tophat2/ffa30bedbee3/env.sh tool_shed.util.common_install_util DEBUG 2014-02-28 09:58:58,216 Attempting to install tool dependency package samtools version 0.1.18. tool_shed.util.tool_dependency_util DEBUG 2014-02-28 09:58:58,256 Updating an existing record for version 0.1.18 of tool dependency samtools for revision ffa30bedbee3 of reposi tory tophat2 by updating the status from Uninstalled to Never installed. [localhost] local: touch ./dependancies/samtools/0.1.18/devteam/tophat2/ffa30bedbee3/env.sh [localhost] local: echo 'if [ -f /software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.18/devteam/package_samtools_0_1_18/171cd8bc208d/env.sh ] ; then . /software/pac kages/galaxy/galaxy-dist/dependancies/samtools/0.1.18/devteam/package_samtools_0_1_18/171cd8bc208d/env.sh ; fi' >> ./dependancies/samtools/0.1.18/devteam/tophat2/ffa30bedbee3/e nv.sh tool_shed.util.common_install_util DEBUG 2014-02-28 09:58:58,438 Attempting to install tool dependency package tophat2 version 2.0.9. tool_shed.util.tool_dependency_util DEBUG 2014-02-28 09:58:58,473 Updating an existing record for version 2.0.9 of tool dependency tophat2 for revision ffa30bedbee3 of reposito ry tophat2 by updating the status from Uninstalled to Never installed. [localhost] local: touch ./dependancies/tophat2/2.0.9/devteam/tophat2/ffa30bedbee3/env.sh [localhost] local: echo 'if [ -f /software/packages/galaxy/galaxy-dist/dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473/env.sh ] ; then . /software/package s/galaxy/galaxy-dist/dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473/env.sh ; fi' >> ./dependancies/tophat2/2.0.9/devteam/tophat2/ffa30bedbee3/env.sh tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:58:58,687 Adding an entry for revision ffa30bedbee3 of repository tophat2 owned by devteam to reposito ry_dependencies_of_installed_repositories. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:58:58,728 Adding an entry for revision ffa30bedbee3 of repository tophat2 owned by devteam to installe d_repository_dependencies_of_installed_repositories. 127.0.0.1 - - [28/Feb/2014:09:58:58 -0300] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/reinstall_reposito ry?id=827fffb0dffdf266" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:58:58,751 Appending revision ffa30bedbee3 of repository tophat2 owned by devteam to all dependent repo sitories in installed_dependent_repositories_of_installed_repositories. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:58:58,763 Adding an entry for revision ffa30bedbee3 of repository tophat2 owned by devteam to tool_dep endencies_of_installed_repositories. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:58:58,789 Adding an entry for revision ffa30bedbee3 of repository tophat2 owned by devteam to installe d_tool_dependencies_of_installed_repositories. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:58:58,800 Adding an entry for version 2.1.0 of package bowtie2 to runtime_tool_dependencies_of_install ed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:58:59,501 Adding an entry for version 2.1.0 of package bowtie2 to installed_runtime_dependent_tool_dep endencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:59:00,300 Adding an entry for version 0.1.18 of package samtools to runtime_tool_dependencies_of_insta lled_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:59:01,006 Adding an entry for version 0.1.18 of package samtools to installed_runtime_dependent_tool_d ependencies_of_installed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:59:01,679 Adding an entry for version 2.0.9 of package tophat2 to runtime_tool_dependencies_of_install ed_tool_dependencies. tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28 09:59:02,617 Adding an entry for version 2.0.9 of package tophat2 to installed_runtime_dependent_tool_dep endencies_of_installed_tool_dependencies. 127.0.0.1 - - [28/Feb/2014:09:58:49 -0300] "POST /admin_toolshed/manage_repositories HTTP/1.1" 302 - "http://localhost:8080/admin_toolshed/reinstall_repository?id=827fffb0dffdf 266" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" 127.0.0.1 - - [28/Feb/2014:09:59:03 -0300] "GET /admin_toolshed/monitor_repository_installation?tool_shed_repository_ids=827fffb0dffdf266 HTTP/1.1" 200 - "http://localhost:8080 /admin_toolshed/reinstall_repository?id=827fffb0dffdf266" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Briand, Sheldon Sent: Thursday, February 27, 2014 8:18 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] tool trouble Hi, I'm having trouble with some of my tools not appearing in the Analyze Data menu. I've successfully installed the tools via the manage installed tool shed repositories(so they are installed to disk). I have tried uninstalling and installing again. The tool installs but does not appear in the menu. Other tools install the menu updates just fine. This is probably due to me corrupting the misbehaving tools installation somehow. I'm guessing that I need to uninstall the tool and wipe some postgres entries. My shed tool path: <toolbox tool_path="../shed_tools"> My current version: parent: 12441:dc067a95261d Added tag release_2014.02.10 for changeset 5e605ed6069f branch: stable Could someone point me in the right direction? Thanks, -Sheldon Sheldon Briand NRC Research Computing Support Analyst Research Computing Support / Soutien Informartique a la Recherche Operations, Science Portfolio / Operations, Portefeuil des sciences SSC-NRC / SPC-CNRC Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford Halifax, NS B3H 3Z1 902 426-1677 sheldon.briand@ssc-spc.gc.ca<mailto:sheldon.briand@ssc-spc.gc.ca>
Hello Briand, This may take some back-and-forth with you to understand the steps you have taken so far. Successfully installing a repository that contains tools usually results in the tools being displayed in the Galaxy tool panel. However, there may be issues that result in the tools not properly loading. This often occurs when you stop and restart your Galaxy instance. Your Galaxy pasxter log will include information about any tool that does not properly load. Uninstalling and reinstalling the repository will usually not have any affect on this. On Feb 28, 2014, at 9:17 AM, "Briand, Sheldon" <Sheldon.Briand@ssc-spc.gc.ca> wrote:
Hi,
I’ve been poking around a bit more. It looks as though galaxy isn’t actually downloading and installing the tools. The tool status changes to installed in the web interface and postgres but the tool is not present on disk.
What is present on disk? If you install a repository with tools, the repository revision's contents should be on disk. However, if the repository is uninstalled, disk files are deleted. Do you have repositories that are installed but do not have any files on disk?
The log below shows no download and make of the tool and dependancies. Hopefully the log gives a bit more information. Sorry for the second email.
tool_shed.util.shed_util_common DEBUG 2014-02-28 09:58:48,567 Updating an existing row for repository 'tophat2' in the tool_shed_repository table, status set to 'New'. tool_shed.util.repository_dependency_util DEBUG 2014-02-28 09:58:48,714 Creating repository dependency objects...
The log looks ok at first inspection, but it's not useful without more information.
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Briand, Sheldon Sent: Thursday, February 27, 2014 8:18 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] tool trouble
Hi,
I’m having trouble with some of my tools not appearing in the Analyze Data menu. I’ve successfully installed the tools via the manage installed tool shed repositories(so they are installed to disk). I have tried uninstalling and installing again.
The above should not be necessary. When you install, are you checking the optional checkboxes to install repository dependencies and tool dependencies? If so, are they installing as well?
The tool installs but does not appear in the menu.
Do you have an example of a repository that contains tools that installls corruptly, but the tools do not load into the tool panel?
Other tools install the menu updates just fine.
Do you have an example of a repsoitory that contains tools that do show up in the tool panel after successfule repository installation?
This is probably due to me corrupting the misbehaving tools installation somehow. I’m guessing that I need to uninstall the tool and wipe some postgres entries.
I strongly advise not manually changing inaything in your database suing sql commands. If you have done this, it could be the cause of the behavor you are describing. The Galaxy UI or API should be used. Greg Von Kuster
My shed tool path: <toolbox tool_path="../shed_tools">
My current version: parent: 12441:dc067a95261d Added tag release_2014.02.10 for changeset 5e605ed6069f branch: stable
Could someone point me in the right direction?
Thanks, -Sheldon
Sheldon Briand NRC Research Computing Support Analyst Research Computing Support / Soutien Informartique a la Recherche Operations, Science Portfolio / Operations, Portefeuil des sciences SSC-NRC / SPC-CNRC Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford Halifax, NS B3H 3Z1 902 426-1677 sheldon.briand@ssc-spc.gc.ca
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participants (2)
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Briand, Sheldon -
Greg Von Kuster