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 <m.vandenbeek@gmail.com> 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 <rmse17@gmail.com> 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 <bjoern.gruening@gmail.com> 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!
>> ___________________________________________________________
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>
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