dependency problem in galaxy server

Issue #76 resolved
Danny created an issue

Hi,

I’m running a local galaxy server instance (on Ubuntu 22.04) for testing purposes and tried to install and use the RepeatExplorer.

Installation completed without errors, but when I want to execute a RepeatExplorer2 clustering, I get the following error:

Collecting package metadata: ...working... done
Solving environment: ...working... failed

PackagesNotFoundError: The following packages are not available from current channels:

  - pillow==9.2.0=pypi_0

Current channels:

  - https://conda.anaconda.org/conda-forge/linux-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/linux-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/linux-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

Is this a problem with galaxy server or with RepeatExplorer?
I don't really know where to start troubleshooting and would appreciate any hints.

Thanks in advance!

Comments (3)

  1. Petr Novak repo owner

    The pillow package is not used by RepeatExplorer so I don’t think is it problem with RepeatExplorer installation. Did you install RepeatExplorer from galaxy toolshed?

  2. Danny reporter

    Thanks for the reply!

    The pillow package is not used by RepeatExplorer […]

    Okay, that's good to know.

    Did you install RepeatExplorer from galaxy toolshed?

    Yes. This is a fresh galaxy server installation (on a fresh ubuntu system) and the only things I’ve installed are RepeatExplorer2 and re_utils:

    This is the whole log output when executing RepeatExplorer:

    galaxy.tools INFO 2022-11-11 08:55:02,549 [pN:main.1,p:3626,tN:WSGI_3] Validated and populated state for tool request (5.174 ms)
    galaxy.tools.actions INFO 2022-11-11 08:55:02,576 [pN:main.1,p:3626,tN:WSGI_3] Handled output named log for tool toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2/repeatexplorer2/2.3.8.1 (5.080 ms)
    galaxy.tools.actions INFO 2022-11-11 08:55:02,578 [pN:main.1,p:3626,tN:WSGI_3] Handled output named ReportArchive for tool toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2/repeatexplorer2/2.3.8.1 (1.930 ms)
    galaxy.tools.actions INFO 2022-11-11 08:55:02,579 [pN:main.1,p:3626,tN:WSGI_3] Handled output named ReportFile for tool toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2/repeatexplorer2/2.3.8.1 (1.461 ms)
    galaxy.tools.actions INFO 2022-11-11 08:55:02,586 [pN:main.1,p:3626,tN:WSGI_3] Added output datasets to history (7.102 ms)
    galaxy.tools.actions INFO 2022-11-11 08:55:02,588 [pN:main.1,p:3626,tN:WSGI_3] Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2/repeatexplorer2/2.3.8.1] complete, ready to be enqueued (1.261 ms)
    galaxy.tools.execute DEBUG 2022-11-11 08:55:02,588 [pN:main.1,p:3626,tN:WSGI_3] Tool toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2/repeatexplorer2/2.3.8.1 created job None (25.084 ms)
    galaxy.web_stack.handlers INFO 2022-11-11 08:55:02,628 [pN:main.1,p:3626,tN:WSGI_3] (Job[id=11,tool_id=toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2/repeatexplorer2/2.3.8.1]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method
    galaxy.tools.execute DEBUG 2022-11-11 08:55:02,633 [pN:main.1,p:3626,tN:WSGI_3] Executed 1 job(s) for tool toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2/repeatexplorer2/2.3.8.1 request (82.957 ms)
    uvicorn.access INFO 2022-11-11 08:55:02,652 [pN:main.1,p:3626,tN:MainThread] 127.0.0.1:55376 - "POST /api/tools HTTP/1.1" 200
    uvicorn.access INFO 2022-11-11 08:55:02,676 [pN:main.1,p:3626,tN:MainThread] 127.0.0.1:55376 - "GET /history/current_history_json?since=2022-11-10T21:53:11.480343 HTTP/1.1" 200
    uvicorn.access INFO 2022-11-11 08:55:02,678 [pN:main.1,p:3626,tN:MainThread] 127.0.0.1:55378 - "GET /api/webhooks HTTP/1.1" 200
    uvicorn.access INFO 2022-11-11 08:55:02,680 [pN:main.1,p:3626,tN:MainThread] 127.0.0.1:55380 - "GET /static/dist/b7327582a95704df7902.png HTTP/1.1" 304
    uvicorn.access INFO 2022-11-11 08:55:02,710 [pN:main.1,p:3626,tN:MainThread] 127.0.0.1:55378 - "GET /api/histories/f597429621d6eb2b/contents?v=dev&limit=1000&q=update_time-ge&qv=2022-11-11T07:54:15.722Z HTTP/1.1" 200
    uvicorn.access INFO 2022-11-11 08:55:02,742 [pN:main.1,p:3626,tN:MainThread] 127.0.0.1:55378 - "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200
    uvicorn.access INFO 2022-11-11 08:55:02,776 [pN:main.1,p:3626,tN:MainThread] 127.0.0.1:55376 - "GET /api/histories/f597429621d6eb2b/contents?v=dev&order=hid&offset=0&limit=100&q=deleted&qv=false&q=visible&qv=true HTTP/1.1" 200
    galaxy.jobs.handler DEBUG 2022-11-11 08:55:03,570 [pN:main.1,p:3626,tN:JobHandlerQueue.monitor_thread] Grabbed Job(s): 11
    galaxy.jobs.mapper DEBUG 2022-11-11 08:55:03,591 [pN:main.1,p:3626,tN:JobHandlerQueue.monitor_thread] (11) Mapped job to destination id: local
    galaxy.jobs.handler DEBUG 2022-11-11 08:55:03,601 [pN:main.1,p:3626,tN:JobHandlerQueue.monitor_thread] (11) Dispatching to local runner
    galaxy.jobs DEBUG 2022-11-11 08:55:03,617 [pN:main.1,p:3626,tN:JobHandlerQueue.monitor_thread] (11) Persisting job destination (destination id: local)
    galaxy.jobs DEBUG 2022-11-11 08:55:03,632 [pN:main.1,p:3626,tN:JobHandlerQueue.monitor_thread] (11) Working directory for job is: /home/galaxy/galaxy/database/jobs_directory/000/11
    galaxy.jobs.runners DEBUG 2022-11-11 08:55:03,638 [pN:main.1,p:3626,tN:JobHandlerQueue.monitor_thread] Job [11] queued (36.447 ms)
    galaxy.jobs.handler INFO 2022-11-11 08:55:03,640 [pN:main.1,p:3626,tN:JobHandlerQueue.monitor_thread] (11) Job dispatched
    galaxy.jobs DEBUG 2022-11-11 08:55:03,718 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Job wrapper for Job [11] prepared (68.277 ms)
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,727 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency last version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,728 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency imagemagick version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,728 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency mafft version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,728 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency blast version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,729 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency diamond version 0.9.29 of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,729 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency blast-legacy version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,729 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency r-igraph version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,730 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency r-data.tree version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,730 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency r-stringr version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,730 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency r-r2html version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,730 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency r-hwriter version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,731 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency r-dt version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,731 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency r-scales version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,731 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency r-plotrix version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,732 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency r-png version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,732 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency r-plyr version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,732 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency r-dplyr version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,733 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency r-optparse version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,733 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency r-dbi version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,733 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency r-rsqlite version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,734 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency r-rserve version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,734 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency bioconductor-biostrings version None of type conda
    galaxy.tool_util.deps DEBUG 2022-11-11 08:55:03,734 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Using dependency pyrserve version 0.9.1 of type conda
    galaxy.tool_util.deps.conda_util DEBUG 2022-11-11 08:55:03,735 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Executing command: /home/galaxy/galaxy/database/dependencies/_conda/bin/conda list --name __last@_uv_ --export > '/home/galaxy/galaxy/database/tmp/jobdeps5k1wpkfpf5b1ffd9bbd17c4e3a89e13c4d97b226d68045d8e833dfa6ccde886c491a397d/__last@_uv_'
    galaxy.tool_util.deps.conda_util DEBUG 2022-11-11 08:55:04,471 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Executing command: /home/galaxy/galaxy/database/dependencies/_conda/bin/conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix /home/galaxy/galaxy/database/jobs_directory/000/11/conda-env --file /home/galaxy/galaxy/database/tmp/jobdeps5k1wpkfpf5b1ffd9bbd17c4e3a89e13c4d97b226d68045d8e833dfa6ccde886c491a397d/__last@_uv_
    Collecting package metadata: ...working... done
    Solving environment: ...working... failed
    
    PackagesNotFoundError: The following packages are not available from current channels:
    
      - pillow==9.2.0=pypi_0
    
    Current channels:
    
      - https://conda.anaconda.org/conda-forge/linux-64
      - https://conda.anaconda.org/conda-forge/noarch
      - https://conda.anaconda.org/bioconda/linux-64
      - https://conda.anaconda.org/bioconda/noarch
      - https://repo.anaconda.com/pkgs/main/linux-64
      - https://repo.anaconda.com/pkgs/main/noarch
      - https://repo.anaconda.com/pkgs/free/linux-64
      - https://repo.anaconda.com/pkgs/free/noarch
      - https://repo.anaconda.com/pkgs/r/linux-64
      - https://repo.anaconda.com/pkgs/r/noarch
    
    To search for alternate channels that may provide the conda package you're
    looking for, navigate to
    
        https://anaconda.org
    
    and use the search bar at the top of the page.
    
    
    galaxy.tool_util.deps.conda_util DEBUG 2022-11-11 08:55:05,106 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] Executing command: /home/galaxy/galaxy/database/dependencies/_conda/bin/conda clean --tarballs -y
    Cache location: 
    There are no tarballs to remove
    galaxy.jobs.runners ERROR 2022-11-11 08:55:05,311 [pN:main.1,p:3626,tN:LocalRunner.work_thread-1] (11) Failure preparing job
    Traceback (most recent call last):
      File "/home/galaxy/galaxy/lib/galaxy/jobs/runners/__init__.py", line 261, in prepare_job
        job_wrapper.runner_command_line = self.build_command_line(
      File "/home/galaxy/galaxy/lib/galaxy/jobs/runners/__init__.py", line 300, in build_command_line
        return build_command(
      File "/home/galaxy/galaxy/lib/galaxy/jobs/command_factory.py", line 71, in build_command
        __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params)
      File "/home/galaxy/galaxy/lib/galaxy/jobs/command_factory.py", line 198, in __handle_dependency_resolution
        if local_dependency_resolution and job_wrapper.dependency_shell_commands:
      File "/home/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 1096, in dependency_shell_commands
        self._dependency_shell_commands = self.tool.build_dependency_shell_commands(
      File "/home/galaxy/galaxy/lib/galaxy/tools/__init__.py", line 2035, in build_dependency_shell_commands
        return self.app.toolbox.dependency_manager.dependency_shell_commands(
      File "/home/galaxy/galaxy/lib/galaxy/tool_util/deps/__init__.py", line 201, in dependency_shell_commands
        return [
      File "/home/galaxy/galaxy/lib/galaxy/tool_util/deps/__init__.py", line 202, in <listcomp>
        dependency.shell_commands()
      File "/home/galaxy/galaxy/lib/galaxy/tool_util/deps/resolvers/conda.py", line 510, in shell_commands
        self.build_environment()
      File "/home/galaxy/galaxy/lib/galaxy/tool_util/deps/resolvers/conda.py", line 505, in build_environment
        raise DependencyException("Conda dependency seemingly installed but failed to build job environment.")
    galaxy.tool_util.deps.resolvers.DependencyException: Conda dependency seemingly installed but failed to build job environment.
    

    But if this isn't a RepeatExplorer issue, it sounds like I should reach out to the Galaxy team.

  3. Log in to comment