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

[mdka00001]

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.

[merelkuijs]

Hi, I'm not affiliated with the steinbock developer team, but this error can likely be resolved by following the installation instructions found at: https://www.ilastik.org/documentation/basics/installation. Once you've installed ilastik, you must find out where the run_ilastik.sh file is. Steinbock is assuming your file is at /opt/ilastik/run_ilastik.sh, but this might not be where the file is actually installed on your computer.

You should then be able to run steinbock classify ilastik run --ilastik [full_path_to_run_ilastik.sh]