From: HONG Z. <hz...@wi...> - 2022-07-13 14:51:41
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Dear Hironori, I did find my issue... I defined my PYTHON path for pytom... it made scipion confused... And all my plugins are installed in the wrong directory... Now I fixed all. Thank you so much for the help:D A+, Hong ________________________________ From: 稲葉弘哲 <hi...@me...> Sent: Wednesday, July 13, 2022 8:37 AM To: Mailing list for Scipion users <sci...@li...> Subject: Re: [scipion-users] emantomo plugin install 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...<mailto:hi...@me...> 2022年7月13日(水) 22:16 HONG ZHAN via scipion-users <sci...@li...<mailto: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...<mailto: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. _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |