Error when running run_pyclone_vi_example1.sh

[nakane-scc]

After installing miniwdl, I ran run_pyclone_vi_example1.sh and got the following error message. How should I deal with this?

Traceback (most recent call last): File "/home/miniconda3/bin/miniwdl", line 10, in sys.exit(main()) File "/home/miniconda3/lib/python3.9/site-packages/WDL/CLI.py", line 73, in main runner(**vars(args)) File "/home/miniconda3/lib/python3.9/site-packages/WDL/CLI.py", line 737, in runner target, input_env, input_json = runner_input( File "/home/miniconda3/lib/python3.9/site-packages/WDL/CLI.py", line 1013, in runner_input v = runner_input_value(s_value, decl.type, downloadable, root) File "/home/miniconda3/lib/python3.9/site-packages/WDL/CLI.py", line 1176, in runner_input_value s_value = validate_input_path(os.path.expanduser(s_value), directory, downloadable, root) File "/home/miniconda3/lib/python3.9/site-packages/WDL/CLI.py", line 1222, in validate_input_path if downloadable and downloadable(path, directory): File "/home/miniconda3/lib/python3.9/site-packages/WDL/CLI.py", line 744, in downloadable=lambda fn, is_dir: runtime.download.able(cfg, fn, directory=is_dir), File "/home/miniconda3/lib/python3.9/site-packages/WDL/runtime/download.py", line 68, in able return bool(uri and _downloader(cfg, uri, directory=directory) is not None) File "/home/miniconda3/lib/python3.9/site-packages/WDL/runtime/download.py", line 56, in _downloader _load(cfg) File "/home/miniconda3/lib/python3.9/site-packages/WDL/runtime/download.py", line 45, in _load for plugin_name, plugin_fn in config.load_plugins(cfg, "file_download"): File "/home/miniconda3/lib/python3.9/site-packages/WDL/runtime/config.py", line 395, in load_plugins yield from ( File "/home/miniconda3/lib/python3.9/site-packages/WDL/runtime/config.py", line 395, in yield from ( File "/home/miniconda3/lib/python3.9/site-packages/WDL/runtime/config.py", line 386, in load_all_plugins importlib_metadata.entry_points().get(f"miniwdl.plugin.{group}", []) AttributeError: 'EntryPoints' object has no attribute 'get'

[pgroves]

Hi,

Can you try to build the docker image from the same version of the code you are trying to run? Just run the script at https://github.com/ncsa/phyloflow/blob/master/pyclone_vi/docker/build_pyclone_vi_container.sh and try again.

I've been away from this project for several months and I'm not sure if the published docker images are up to date with the wdl tasks in the code base.

If that doesn't work, we can dig deeper.

-Peter

[nakane-scc]

Thank you for your response.

When you run the "build_pyclone_vi_container.sh" script, you will see the following error message

failed to solve with frontend dockerfile.v0: failed to read dockerfile: open /var/lib/docker/tmp/buildkit-mount2218653516/Dockerfile-pyclone-vi: no such file or directory.

I have Ubuntu 20.04LTS installed on WSL2, could this environment be causing the error?

[ChuanyiZ]

Hi, Could you try setting these environment variables in the terminal before running build_pyclone_vi_container.sh?

export DOCKER_BUILDKIT=0
export COMPOSE_DOCKER_CLI_BUILD=0