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[Errno 2] No such file or directory: '/opt/ilastik/run_ilastik.sh' #278

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mdka00001 opened this issue Mar 5, 2025 · 0 comments
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@mdka00001
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mdka00001 commented Mar 5, 2025

While executing the following command:
steinbock classify ilastik run

I am getting the following error:

  File "/home/mdka00001/miniconda3/envs/imc_analysis/bin/steinbock", line 10, in <module>
    sys.exit(steinbock_cmd_group())
             ^^^^^^^^^^^^^^^^^^^^^
  File "/home/mdka00001/miniconda3/envs/imc_analysis/lib/python3.12/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mdka00001/miniconda3/envs/imc_analysis/lib/python3.12/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/mdka00001/miniconda3/envs/imc_analysis/lib/python3.12/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mdka00001/miniconda3/envs/imc_analysis/lib/python3.12/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mdka00001/miniconda3/envs/imc_analysis/lib/python3.12/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mdka00001/miniconda3/envs/imc_analysis/lib/python3.12/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mdka00001/miniconda3/envs/imc_analysis/lib/python3.12/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mdka00001/miniconda3/envs/imc_analysis/lib/python3.12/site-packages/steinbock/_cli/utils.py", line 34, in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/mdka00001/miniconda3/envs/imc_analysis/lib/python3.12/site-packages/steinbock/_env.py", line 42, in use_ilastik_env_wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/mdka00001/miniconda3/envs/imc_analysis/lib/python3.12/site-packages/steinbock/classification/_cli/ilastik.py", line 240, in run_cmd
    result = ilastik.run_pixel_classification(
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mdka00001/miniconda3/envs/imc_analysis/lib/python3.12/site-packages/steinbock/classification/ilastik/_ilastik.py", line 284, in run_pixel_classification
    result = run_captured(args, env=ilastik_env)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/mdka00001/miniconda3/envs/imc_analysis/lib/python3.12/site-packages/steinbock/_env.py", line 12, in run_captured
    with subprocess.Popen(
         ^^^^^^^^^^^^^^^^^
  File "/home/mdka00001/miniconda3/envs/imc_analysis/lib/python3.12/subprocess.py", line 1026, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/home/mdka00001/miniconda3/envs/imc_analysis/lib/python3.12/subprocess.py", line 1953, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: '/opt/ilastik/run_ilastik.sh'

I tried with both conda package and pip package. Getting error in both.

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