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nanoporetech / tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.

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Fail to Install tombo using venv3 Ubuntu18.04

abadouh opened this issue · comments

commented

Hey,
I am trying to install tombo using pip and or the git repository and I get the same error.
Below you can find the details:

OS: Ubuntu18.04
Python: 3.8
numpy: 1.24.4

Using pip

mkdir tombo 
python3 -m venv venv3
source venv3/bin/activate
pip install --upgrade pip
pip install numpy
pip install ont-tombo[full]

Using github

git clone https://github.com/nanoporetech/tombo 
cd tombo/
python3 -m venv venv3
source venv3/bin/activate
pip install --upgrade pip
pip install numpy
pip install -e .

I get the following error:

Obtaining file:///home/workspaces/benchmark/tombo/tombo
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build editable ... done
  Installing backend dependencies ... done
  Preparing editable metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Preparing editable metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [34 lines of output]
      ************************************************************
      INSTALLATION ERROR:
          Need to install numpy before tombo installation.
          This is required in order to get maximum efficincy from cython code optimizations.
      To install run:
      $ pip install numpy
      ************************************************************
      /tmp/pip-build-env-9yil7j94/overlay/lib/python3.8/site-packages/setuptools/build_meta.py:487: SetuptoolsDeprecationWarning: Running `setup.py` directly as CLI tool is deprecated.
      !!
      
              ********************************************************************************
              Please avoid using `sys.exit(0)` or similar statements that don't fit in the paradigm of a configuration file.
      
              See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
              ********************************************************************************
      
      !!
        super().run_setup(setup_script=setup_script)
      Traceback (most recent call last):
        File "/home/workspaces/benchmark/tombo/tombo/venv3/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/home/workspaces/benchmark/tombo/tombo/venv3/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/home/workspaces/benchmark/tombo/tombo/venv3/lib/python3.8/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 181, in prepare_metadata_for_build_editable
          return hook(metadata_directory, config_settings)
        File "/tmp/pip-build-env-9yil7j94/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 453, in prepare_metadata_for_build_editable
          return self.prepare_metadata_for_build_wheel(
        File "/tmp/pip-build-env-9yil7j94/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 368, in prepare_metadata_for_build_wheel
          self._bubble_up_info_directory(metadata_directory, ".egg-info")
        File "/tmp/pip-build-env-9yil7j94/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 337, in _bubble_up_info_directory
          info_dir = self._find_info_directory(metadata_directory, suffix)
        File "/tmp/pip-build-env-9yil7j94/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 348, in _find_info_directory
          assert len(candidates) == 1, f"Multiple {suffix} directories found"
      AssertionError: Multiple .egg-info directories found
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
commented

It appears as though pip is not finding the numpy install. This may be an issue with your python environment or the way Tombo runs setup. Tombo is deprecated and I would recommend moving to Remora for raw signal analysis.