Re: [scipion-users] emantomo plugin install

[稲葉弘哲 <hi...@me...>]

Dear Hong

As David mentioned, adding "CONDA_ACTIVATION_CMD"  to the config was
necessary for EMAN and Pyseg installation when I installed them.
In my case, "CONDA_ACTIVATION_CMD = .
/usr/local/miniconda/etc/profile.d/conda.sh" worked.
See also Topaz integration in https://github.com/scipion-em/scipion-em-topaz

Best,
Hironori

Hironori Inaba Ph.d.
Department of Histology and Cell Biology,
Graduate School of Medicine, Mie University, Japan
e-mail: hi...@me...

2022年7月13日(水) 22:16 HONG ZHAN via scipion-users <
sci...@li...>:

> Thanks Grigory and David,
>
> I tried also adding the this line in scipion.conf, however the issue
> persisted. I also have installed eman2.91 before, it might miss things up.
> I will check my envs and if not, i will rebuild my system clean.
>
> Pesyg seems having same issue…
>
> Thank you so much for the reply.
>
> Bien cordialement,
> Hong
>
> On Jul 13, 2022, at 1:43 AM, David Herreros <dhe...@cn...> wrote:
>
> 
>
> 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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