Re: [scipion-users] error during test sphire

[Pablo C. <pc...@cn...>]

Hi Anne.

Try setting the CONDA_ACTIVATION_CMD variable like:

CONDA_ACTIVATION_CMD = . /opt/conda/etc/profile.d/conda.sh


Mind the dot (.).

If that doesn't work try:

CONDA_ACTIVATION_CMD = source /opt/conda/etc/profile.d/conda.sh

On 30/11/20 17:00, Anne-Pascale JAUDIER wrote:
> Hi,
>
> I try the following test with the following  error on the command "conda activate"
> The command "conda activate" is working in a interactive shell.
>
> Thanks,
> Anne-Pascale
>
>   scipion tests sphire.tests.test_protocol_janni
>
>>>> ERROR running protocol sphire - janni denoising
>      FAILED with error: Protocol failed: Command '/opt/conda/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && janni_denoise.py denoise Runs/000146_SphireProtJanniDenoising/tmp/ Runs/000146_SphireProtJanniDenoising/tmp/ /data/sics/scipion/software/em/janni_model-20190703/gmodel_janni_20190703.h5' returned non-zero exit status 1.
>
> *************** LAST 50 LINES OF THE LOG *********************
>
>        threads: 1
>   Starting at step: 1
>   Running steps
> STARTED: denoisingStep, step 1, time 2020-11-30 18:21:48.558591
> /opt/conda/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && janni_denoise     .py denoise Runs/000146_SphireProtJanniDenoising/tmp/ Runs/000146_SphireProtJann     iDenoising/tmp/ /data/sics/scipion/software/em/janni_model-20190703/gmodel_janni     _20190703.h5
>
> 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
> -------------------------------
>
> ----------------------------------------------------------------------
> Anne-Pascale Jaudier
> SICS – I2BC
> Bat 34 - 1 avenue de la terrasse - 91198 Gif sur Yvette
> 01 69 82 34 74
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*