Galaxy server requires a restart to activate tools

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Galaxy server requires a restart to activate tools

RMSe17
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!
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Re: Galaxy server requires a restart to activate tools

Björn Grüning-3
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/
>
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Re: Galaxy server requires a restart to activate tools

RMSe17
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 <[hidden email]> 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/
>>
>
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Re: Galaxy server requires a restart to activate tools

Marius van den Beek
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 <[hidden email]> 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 <[hidden email]> 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/


___________________________________________________________
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Re: Galaxy server requires a restart to activate tools

RMSe17
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 tool configuration /service/galaxy/server/shed_tool_conf.xml
galaxy.tools.toolbox.base INFO 2017-09-20 13:53:01,771 Parsing the tool configuration /service/galaxy/server/migrated_tools_conf.xml
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,772 Reading tools from config files finshed (22.948 ms)
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,772 Loading section: Get Data
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,774 Loading section: Send Data
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,775 Loading section: Collection Operations
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,775 Loading section: Lift-Over
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,776 Loading section: Text Manipulation
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,777 Loading section: Filter and Sort
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,778 Loaded label: GFF
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,778 Loading section: Join, Subtract and Group
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,779 Loading section: Convert Formats
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,780 Loading section: Extract Features
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,781 Loading section: Fetch Sequences
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,781 Loading section: Fetch Alignments
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,782 Loading section: Statistics
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,783 Loading section: Graph/Display Data
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,783 Loading section: NGS: QC and manipulation
galaxy.tools.toolbox.base DEBUG 2017-09-20 13:53:01,784 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 13:53:01,784 Loading tool panel finished (12.560 ms)
galaxy.tools.deps DEBUG 2017-09-20 13:53:01,788 Unable to find config file './dependency_resolvers_conf.xml'
galaxy.datatypes.registry DEBUG 2017-09-20 13:53:01,821 Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2017-09-20 13:53:01,822 Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2017-09-20 13:53:01,824 Loaded history export tool: __EXPORT_HISTORY__
galaxy.queue_worker INFO 2017-09-20 13:53:01,824 Queuing async task rebuild_toolbox_search_index for main.1.
galaxy.queue_worker DEBUG 2017-09-20 13:53:01,830 Toolbox reload (107.763 ms)
Fetching package metadata ...galaxy.queue_worker INFO 2017-09-20 13:53:02,555 Instance 'main.2' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.tools.search DEBUG 2017-09-20 13:53:02,556 Starting to build toolbox index.
galaxy.tools.search DEBUG 2017-09-20 13:53:02,712 Toolbox index finished (156.568 ms)
galaxy.queue_worker INFO 2017-09-20 13:53:02,738 Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.tools.search DEBUG 2017-09-20 13:53:02,738 Starting to build toolbox index.
galaxy.tools.search DEBUG 2017-09-20 13:53:02,800 Toolbox index finished (62.414 ms)
............
Solving package specifications: ..........

Package plan for installation in environment /service/galaxy/deps/_conda/envs/__fastqc@0.11.5:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    openjdk-8.0.121            |                1        64.2 MB
    perl-5.22.0.1              |                0        15.1 MB  conda-forge
    fastqc-0.11.5              |       pl5.22.0_2         9.5 MB  bioconda
    ------------------------------------------------------------
                                           Total:        88.8 MB

The following NEW packages will be INSTALLED:

    fastqc:  0.11.5-pl5.22.0_2 bioconda
    openjdk: 8.0.121-1
    perl:    5.22.0.1-0        conda-forge

Fetching packages ...
openjdk-8.0.12 100% |###############################| Time: 0:00:02  27.25 MB/s
perl-5.22.0.1- 100% |###############################| Time: 0:00:02   7.35 MB/s
fastqc-0.11.5- 100% |###############################| Time: 0:00:02   4.19 MB/s
Extracting packages ...
[      COMPLETE      ]|##################################################| 100%
Linking packages ...
[      COMPLETE      ]|##################################################| 100%
#
# To activate this environment, use:
# > source activate __fastqc@0.11.5
#
# To deactivate this environment, use:
# > source deactivate __fastqc@0.11.5
#

galaxy.tools.deps DEBUG 2017-09-20 13:53:30,604 Using dependency fastqc version 0.11.5 of type conda

--------
Here are the logs from subsequent run attempt without Galaxy restart:
galaxy.tools DEBUG 2017-09-20 13:54:25,393 Validated and populated state for tool request (19.376 ms)
galaxy.util.object_wrapper WARNING 2017-09-20 13:54:25,421 Unable to create dynamic subclass for <type 'instance'>, None: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases
galaxy.tools.actions INFO 2017-09-20 13:54:25,437 Handled output named html_file for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69 (16.435 ms)
galaxy.tools.actions INFO 2017-09-20 13:54:25,454 Handled output named text_file for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69 (16.543 ms)
galaxy.tools.actions INFO 2017-09-20 13:54:25,459 Added output datasets to history (4.344 ms)
galaxy.tools.actions INFO 2017-09-20 13:54:25,473 Verified access to datasets for Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69] (7.722 ms)
galaxy.tools.actions INFO 2017-09-20 13:54:25,474 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69] complete, ready to flush (15.496 ms)
galaxy.tools.actions INFO 2017-09-20 13:54:25,497 Flushed transaction for job Job[id=7,tool_id=toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69] (22.464 ms)
galaxy.tools.execute DEBUG 2017-09-20 13:54:25,497 Tool [toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69] created job [7] (85.774 ms)
galaxy.tools.execute DEBUG 2017-09-20 13:54:25,503 Executed 1 job(s) for tool toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69 request: (109.782 ms)
galaxy.jobs DEBUG 2017-09-20 13:54:26,059 (7) Working directory for job is: /service/galaxy/data/jobs/000/7
galaxy.jobs.handler WARNING 2017-09-20 13:54:26,060 (7) Tool 'toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69' removed from tool config, unable to run job
galaxy.model.metadata DEBUG 2017-09-20 13:54:26,216 Cleaning up external metadata files
galaxy.jobs.handler ERROR 2017-09-20 13:54:26,243 (7) Error checking job readiness

Thanks!

On Tue, Sep 19, 2017 at 10:06 AM, Marius van den Beek <[hidden email]> wrote:
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 <[hidden email]> 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 <[hidden email]> 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:
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To search Galaxy mailing lists use the unified search at:
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