Re: [scipion-users] emantomo plugin install

[HONG Z. <hz...@wi...>]

Dear Wolfgang and all,

Apparently, my PYTHON path was messed up with pytom... And all my plugins are installed in the wrong directory... Now I fixed all. I am glad not to rebuild system...

Thank you so much for the help and have a great day !


A+,

Hong
________________________________
From: Lugmayr, Wolfgang <w.l...@uk...>
Sent: Wednesday, July 13, 2022 9:07 AM
To: Mailing list for Scipion users <sci...@li...>
Subject: Re: [scipion-users] emantomo plugin install

Dear Hong,

maybe it was not so clear, but the conda activation is in the PLUGINS section below the PYWORKFLOW in the config file.
In our case:
:
[PLUGINS]
CONDA_ACTIVATION_CMD = source /beegfs/cssb/software/em/scipion/3.0/miniconda/etc/profile.d/conda.sh
EM_ROOT = software/em
:
CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6
:

Cheers,
Wolfgang


________________________________
From: "Mailing list for Scipion users" <sci...@li...>
To: "Mailing list for Scipion users" <sci...@li...>
Cc: "HONG ZHAN" <hz...@wi...>
Sent: Wednesday, 13 July, 2022 15:14:35
Subject: [EXT] Re: [scipion-users] emantomo plugin install

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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