Try to update test instance #202
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Idea is that we build bundles against the existing servers, then just pull the bundles into an instance that can write to cvmfs.
jmchilton
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Hit road block on dependency resolution not being setup in the container... tried turning on auto init but... toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/fetch_genome_all_fasta_dbkeys/0.0.1\ngalaxy.queue_worker DEBUG 2023-07-05 22:59:37,048 [pN:main.1,p:78,tN:Thread-1] Data managers reloaded (190.271 ms)\ngalaxy.tool_shed.galaxy_install.install_manager ERROR 2023-07-05 22:59:37,061 [pN:main.1,p:78,tN:WSGI_0] Error installing repository 'data_manager_fetch_genome_dbkeys_all_fasta'\nTraceback (most recent call last):\n File "/galaxy/server/lib/galaxy/tool_shed/galaxy_install/install_manager.py", line 511, in install_repositories\n self.install_tool_shed_repository(\n File "/galaxy/server/lib/galaxy/tool_shed/galaxy_install/install_manager.py", line 641, in install_tool_shed_repository\n [self._view.install_dependencies(r) for r in new_requirements]\n File "/galaxy/server/lib/galaxy/tool_shed/galaxy_install/install_manager.py", line 641, in \n [self._view.install_dependencies(r) for r in new_requirements]\n File "/galaxy/server/lib/galaxy/tool_util/deps/views.py", line 144, in install_dependencies\n return self._dependency_manager._requirements_to_dependencies_dict(requirements, **kwds)\n File "/galaxy/server/lib/galaxy/tool_util/deps/init.py", line 282, in _requirements_to_dependencies_dict\n dependencies = resolve(\n File "/galaxy/server/lib/galaxy/tool_util/deps/resolvers/conda.py", line 246, in resolve_all\n is_installed = self.install_all(conda_targets)\n File "/galaxy/server/lib/galaxy/tool_util/deps/resolvers/conda.py", line 186, in install_all\n return_code = install_conda_targets(conda_targets, conda_context=self.conda_context, env_name=env)\n File "/galaxy/server/lib/galaxy/tool_util/deps/conda_util.py", line 543, in install_conda_targets\n return conda_context.exec_create(create_args, allow_local=allow_local)\n File "/galaxy/server/lib/galaxy/tool_util/deps/conda_util.py", line 293, in exec_create\n if self.conda_version >= Version("4.7.5"):\n File "/galaxy/server/lib/galaxy/tool_util/deps/conda_util.py", line 145, in conda_version\n self._guess_conda_properties()\n File "/galaxy/server/lib/galaxy/tool_util/deps/conda_util.py", line 157, in _guess_conda_properties\n info = self.conda_info()\n File "/galaxy/server/lib/galaxy/tool_util/deps/conda_util.py", line 197, in conda_info\n info_out = commands.execute(cmd)\n File "/galaxy/server/lib/galaxy/util/commands.py", line 104, in execute\n return _wait(cmds, input=input, shell=False, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)\n File "/galaxy/server/lib/galaxy/util/commands.py", line 121, in _wait\n p = subprocess.Popen(cmds, **popen_kwds)\n File "/usr/local/lib/python3.10/subprocess.py", line 971, in init\n self._execute_child(args, executable, preexec_fn, close_fds,\n File "/usr/local/lib/python3.10/subprocess.py", line 1863, in _execute_child\n raise child_exception_type(errno_num, err_msg, err_filename)\nFileNotFoundError: [Errno 2] No such file or directory: '/galaxy/server/database/dependencies/_conda/bin/conda'\ngalaxy.tool_shed.util.repository_util DEBUG 2023-07-05 22:59:37,064 [pN:main.1,p:78,tN:WSGI_0] Removed repository installation directory: /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/4d3eff1bc421\nuvicorn.access INFO 2023-07-05 22:59:37,076 [pN:main.1,p:78,tN:MainThread] 172.17.0.1:53660 - "POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1" 200\ngalaxy.tools.cache DEBUG 2023-07-05 22:59:37,641 [pN:main.1,p:78,tN:Thread-3 (check)] Removed the following tools from cache: ['toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.4', \ Opps... pyh38be061_0.conda\nExtracting conda-23.1.0-py310hff52083_0.conda\nExtracting mamba-1.4.2-py310h51d5547_0.conda\ngalaxy.tool_util.deps.installable WARNING 2023-07-05 22:59:20,261 [pN:main,p:12,tN:MainThread] Conda installation requested and failed.\ngalaxy.tool_util.deps.conda_util WARNING 2023-07-05 22:59:20,267 [pN:main,p:12,tN:MainThread] Cannot install Conda because conda_prefix '/galaxy/server/database/dependencies/_conda' exists and is not empty.\ |
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I've picked out the commits we still want from this in #211, closing this to avoid confusion. |
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