Re: [scipion-users] emantomo plugin install

[David H. <dhe...@cn...>]

Dear Hong,


It seems Scipion is not able to find the location of conda in your 
system, which is required to execute the programs integrated in emantomo.


The easiest way to solve this issue is to add a new variable to the 
Scipion config file. This file should be located in 
path/to/your/scipion/config/scipion.conf


The variable you will need is the following one (after the [PYWORKFLOW] 
section inside the file should be fine): CONDA_ACTIVATION_CMD = eval 
"$(/path/to/your/conda/condabin/conda shell.bash hook)".


Best,


David


On 12/7/22 20:43, HONG ZHAN via scipion-users wrote:
> Hi all,
>
> I am trying to install emantomo plugin, however, it showed error 
> message below, does anyone have idea how to solve this error?
>
> Super thanks!
> Hong
>
> --------------------
> CommandNotFoundError: Your shell has not been properly configured to 
> use 'conda activate'.
> To initialize your shell, run
>
>     $ conda init <SHELL_NAME>
>
> Currently supported shells are:
>   - bash
>   - fish
>   - tcsh
>   - xonsh
>   - zsh
>   - powershell
>
> See 'conda init --help' for more information and options.
>
> IMPORTANT: You may need to close and restart your shell after running 
> 'conda init'.
>
>
> Traceback (most recent call last):
>   File 
> "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 201, in run
>     self._run()
>   File 
> "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 252, in _run
>     resultFiles = self._runFunc()
>   File 
> "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 248, in _runFunc
>     return self._func(*self._args)
>   File 
> "/home/hong/scipion-em-emantomo/emantomo/protocols/protocol_tomo_template_match.py", 
> line 135, in preprocess
>     self.runJob(program, '%s %s --apix=%f' % (tomo.getFileName(), 
> tomoFile, tomo.getSamplingRate()),
>   File 
> "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 1454, in runJob
>     self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
>   File 
> "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", 
> line 65, in runJob
>     process.runJob(log, programName, params,
>   File 
> "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", 
> line 52, in runJob
>     return runCommand(command, env, cwd)
>   File 
> "/opt/anaconda3/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", 
> line 67, in runCommand
>     check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
>   File "/opt/anaconda3/envs/scipion3/lib/python3.8/subprocess.py", 
> line 364, in check_call
>     raise CalledProcessError(retcode, cmd)
> subprocess.CalledProcessError: Command '  conda activate 
> emantomo-2.91_211111 && e2proc3d.py 
>  Runs/000002_ProtImportTomograms/extra/overview_wbp.em 
> /home/hong/ScipionUserData/projects/TestEmanTomoTempMatch/Runs/000198_EmanProtTomoTempMatch/tmp/overview_wbp.mrc 
> --apix=5.000000' returned non-zero exit status 1.
>
>
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