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Relion5.0 tomo #1087

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nbcronin opened this issue Mar 1, 2024 · 12 comments
Open

Relion5.0 tomo #1087

nbcronin opened this issue Mar 1, 2024 · 12 comments

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@nbcronin
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nbcronin commented Mar 1, 2024

Installed Relion5.0. with no problem. Runs with programs in the environment.yml (relion_blush; topaz etc)

Currently want to run relion --tomo ( Relion-5.0-beta-1-commit-b75b38) and get the error

---------------------------------- PYTHON ERROR ---------------------------------
Has RELION been provided a Python interpreter with the correct environment?
The interpreter can be passed to RELION either during Cmake configuration by
using the Cmake flag -DPYTHON_EXE_PATH=<path/to/python/interpreter>.

Using python executable: /opt/anaconda3/envs/relion-5.0/bin/python

ModuleNotFoundError: No module named 'tomography_python_programs'

The path for the python executable is correct - is there a module named tomography_python_programs?

Thanks

Nora
@nbcronin
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nbcronin commented Mar 4, 2024

I can see the tomo programs are located - in a relion/src/tomography_python_programs - ie there an environment variable to point to this? Currently it is looking at the conda environment to locate the programs.

nora

@LIjieHan
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I'm having the same problem, did you figure out how to fix it?

@biochem-fan biochem-fan mentioned this issue Mar 20, 2024
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@nbcronin
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nbcronin commented Mar 21, 2024 via email

@Qiangong2
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The files are successfully made in the bin directory, but we still get the python error.

@nbcronin
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nbcronin commented Mar 25, 2024 via email

@Qiangong2
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Hi @nbcronin, No, dynamight is functional, but the other tomo python programs do not. The conda paths are fine, Relion is able to find the correct python path during compilation and any other tools except for the tomo tools.

@Qiangong2
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@biochem-fan Any ideas?

@EricDeveaud
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hello,
had the same problem with relion-5.0 and found that among this python module some other are missing,
I fixed it by.

    # used by relion_python_tomo_align_tilt_series
    cd $(SOFT)/src && cp -r tomography_python_programs $(PYLIB)
    $(PIP) install makefun yet_another_imod_wrapper lil_aretomo
    # used by relion_python_tomo_get_particle_poses
    $(PIP) install morphosamplers
    # used by relion_python_tomo_pick
    $(PIP) install napari_threedee
    # used by relion_python_tomo_pick relion_python_tomo_view relion_python_tomo_exclude_tilt_images
    $(PIP) install lru-dict

NB installation performed out of conda.

@nbcronin
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nbcronin commented Apr 22, 2024 via email

@Qiangong2
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Hi @nbcronin

Unfortunately, it still doesn't work.

---------------------------------- PYTHON ERROR ---------------------------------
   Has RELION been provided a Python interpreter with the correct environment?
   The interpreter can be passed to RELION either during Cmake configuration by
     using the Cmake flag -DPYTHON_EXE_PATH=<path/to/python/interpreter>.
---------------------------------------------------------------------------------

The above error appears specifically on relion_python_tomo_import, relion_python_tomo_denoise, relion_python_tomo_exclude_tilt_images, relion_python_modelangelo, relion_python_topaz, and relion_python_tomo_align_tilt_series. The other python tools are fine.

@biochem-fan Can you please provide an update on this?

@biochem-fan
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@Qiangong2 I am not involved in the tomography aspect of RELION, so I cannot help.

@Qiangong2
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@Qiangong2 I am not involved in the tomography aspect of RELION, so I cannot help.

@biochem-fan Who is then?

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5 participants
@biochem-fan @EricDeveaud @Qiangong2 @LIjieHan @nbcronin