dependency problem in galaxy server
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)
-
repo owner -
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.
-
reporter - changed status to resolved
galaxy server issue
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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?