Re: [galaxy-dev] Galaxy server requires a restart to activate tools
Hi Marius, Using commit 03d9a9c (03d9a9c6fba0e26fae080a7ebb65fd6f0676477e) on release_17.0. All newly installed tools appear to be doing this. Here are the logs from fastqc tool install: galaxy.tools.deps DEBUG 2017-09-20 13:52:45,583 Dependency fastqc not found. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-09-20 13:52:55,274 Creating repository dependency objects... galaxy.tools.toolbox.base DEBUG 2017-09-20 13:52:56,043 Appending to tool panel section: NGS: QC and manipulation tool_shed.util.repository_util DEBUG 2017-09-20 13:52:56,048 Adding new row for repository 'fastqc' in the tool_shed_repository table, status set to 'New'. tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2017-09-20 13:52:56,057 Building repository dependency relationships... galaxy.tools.toolbox.base DEBUG 2017-09-20 13:52:56,058 Appending to tool panel section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-09-20 13:52:56,516 Appending to tool panel section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:00,715 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69, version: 0.69 into tool panel galaxy.tools.toolbox.watcher DEBUG 2017-09-20 13:53:01,537 The file '/service/galaxy/server/shed_tool_conf.xml' has changes. galaxy.queue_worker DEBUG 2017-09-20 13:53:01,540 Executing toolbox reload on 'main.2' galaxy.tools.toolbox.base INFO 2017-09-20 13:53:01,564 Parsing the tool configuration /service/galaxy/server/config/tool_conf.xml.sample galaxy.tools.toolbox.base ERROR 2017-09-20 13:53:01,577 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base INFO 2017-09-20 13:53:01,583 Parsing the tool configuration /service/galaxy/server/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2017-09-20 13:53:01,586 Parsing the tool configuration /service/galaxy/server/migrated_tools_conf.xml galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,586 Reading tools from config files finshed (21.990 ms) galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,586 Loading section: Get Data galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,589 Loading section: Send Data galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,589 Loading section: Collection Operations galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,590 Loading section: Lift-Over galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,590 Loading section: Text Manipulation galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,592 Loading section: Filter and Sort galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,592 Loaded label: GFF galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,593 Loading section: Join, Subtract and Group galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,593 Loading section: Convert Formats galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,595 Loading section: Extract Features galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,596 Loading section: Fetch Sequences galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,596 Loading section: Fetch Alignments galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,597 Loading section: Statistics galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,598 Loading section: Graph/Display Data galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,598 Loading section: NGS: QC and manipulation galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,599 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69, version: 0.69 into tool panel galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,599 Loading tool panel finished (13.125 ms) galaxy.tools.deps DEBUG 2017-09-20 13:53:01,604 Unable to find config file './dependency_resolvers_conf.xml' galaxy.datatypes.registry DEBUG 2017-09-20 13:53:01,641 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2017-09-20 13:53:01,643 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2017-09-20 13:53:01,645 Loaded history export tool: __EXPORT_HISTORY__ galaxy.queue_worker INFO 2017-09-20 13:53:01,645 Queuing async task rebuild_toolbox_search_index for main.2. galaxy.queue_worker DEBUG 2017-09-20 13:53:01,652 Toolbox reload (112.130 ms) galaxy.tools.toolbox.watcher DEBUG 2017-09-20 13:53:01,719 The file '/service/galaxy/server/shed_tool_conf.xml' has changes. galaxy.queue_worker DEBUG 2017-09-20 13:53:01,722 Executing toolbox reload on 'main.1' galaxy.tools.deps.conda_util DEBUG 2017-09-20 13:53:01,734 Executing command: /service/galaxy/deps/_conda/bin/conda create -y --name __fastqc@0.11.5 fastqc=0.11.5 galaxy.tools.toolbox.base INFO 2017-09-20 13:53:01,749 Parsing the tool configuration /service/galaxy/server/config/tool_conf.xml.sample galaxy.tools.toolbox.base ERROR 2017-09-20 13:53:01,760 Error reading tool configuration file from path: extract/liftOver_wrapper.xml galaxy.tools.toolbox.base INFO 2017-09-20 13:53:01,765 Parsing the too
Re: [galaxy-dev] Galaxy server requires a restart to activate tools
Hi, Can you check the commit of galaxy that you are using and post the logs that you see when you install a tool that doesn't work ? Does this happen for all tools that you install ? Best, Marius On 19 September 2017 at 15:40, RMSe17 wrote: > Hi Bjoern, > > I upgraded to 17.05, but am still getting the same error when trying > to run an installed tool without Galaxy restart. > > Any idea on where the issue could be? > > Thanks! > > On 9/13/17, Björn Grüning wrote: > > Hi, > > > > afaik Marius fixed a few bugs in 17.05 and I know that 17.05 should work > > as described not sure 17.01 can be exprected to work this way. > > > > Can you try 17.05? > > Thanks, > > Bjoern > > > > On 14.09.2017 03:51, RMSe17 wrote: > >> Hello, I have a fresh 17.01 Galaxy installed and set up with uWSGI. > >> After installing a new tool, I can't run it without first restarting > >> Galaxy. This is odd, because I know in 17.01 that should no longer be > >> happening. > >> > >> The error I get is "This tool was disabled before job completed. > >> Please contact your Galaxy administrator. > >> > >> In the logs I see "Tool (... tool name) removed from tool config, > >> unable to run job > >> Cleaning up external metadata files > >> Error checking job readiness" > >> > >> After Galaxy restarts, the tool runs fine. > >> > >> Is there anything typical that could cause this? Any place I should > >> start looking? > >> > >> Thanks! > >> ___ > >> 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: > >> https://lists.galaxyproject.org/ > >> > >> To search Galaxy mailing lists use the unified search at: > >> http://galaxyproject.org/search/ > >> > > > ___ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] Galaxy server requires a restart to activate tools
Hi Bjoern, I upgraded to 17.05, but am still getting the same error when trying to run an installed tool without Galaxy restart. Any idea on where the issue could be? Thanks! On 9/13/17, Björn Grüning wrote: > Hi, > > afaik Marius fixed a few bugs in 17.05 and I know that 17.05 should work > as described not sure 17.01 can be exprected to work this way. > > Can you try 17.05? > Thanks, > Bjoern > > On 14.09.2017 03:51, RMSe17 wrote: >> Hello, I have a fresh 17.01 Galaxy installed and set up with uWSGI. >> After installing a new tool, I can't run it without first restarting >> Galaxy. This is odd, because I know in 17.01 that should no longer be >> happening. >> >> The error I get is "This tool was disabled before job completed. >> Please contact your Galaxy administrator. >> >> In the logs I see "Tool (... tool name) removed from tool config, >> unable to run job >> Cleaning up external metadata files >> Error checking job readiness" >> >> After Galaxy restarts, the tool runs fine. >> >> Is there anything typical that could cause this? Any place I should >> start looking? >> >> Thanks! >> ___ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/ >> > ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] Galaxy server requires a restart to activate tools
Hi, afaik Marius fixed a few bugs in 17.05 and I know that 17.05 should work as described not sure 17.01 can be exprected to work this way. Can you try 17.05? Thanks, Bjoern On 14.09.2017 03:51, RMSe17 wrote: > Hello, I have a fresh 17.01 Galaxy installed and set up with uWSGI. > After installing a new tool, I can't run it without first restarting > Galaxy. This is odd, because I know in 17.01 that should no longer be > happening. > > The error I get is "This tool was disabled before job completed. > Please contact your Galaxy administrator. > > In the logs I see "Tool (... tool name) removed from tool config, > unable to run job > Cleaning up external metadata files > Error checking job readiness" > > After Galaxy restarts, the tool runs fine. > > Is there anything typical that could cause this? Any place I should > start looking? > > Thanks! > ___ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Galaxy server requires a restart to activate tools
Hello, I have a fresh 17.01 Galaxy installed and set up with uWSGI. After installing a new tool, I can't run it without first restarting Galaxy. This is odd, because I know in 17.01 that should no longer be happening. The error I get is "This tool was disabled before job completed. Please contact your Galaxy administrator. In the logs I see "Tool (... tool name) removed from tool config, unable to run job Cleaning up external metadata files Error checking job readiness" After Galaxy restarts, the tool runs fine. Is there anything typical that could cause this? Any place I should start looking? Thanks! ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
