How to activate conda environment that was created using a .yml file? #506
Comments
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Note: It is currently possible to post-hoc activate the custom environment by executing csp@5b5b1344459e:/$ conda activate csp
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'. |
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2nd note: Even after adding to the latest script it still does not work. Which makes me think that it must have something to do with the different neurodocker versions ( generate_docker() {
docker run -i --rm repronim/neurodocker:0.9.4 generate docker \
--base-image neurodebian:stretch-non-free \
--arg DEBIAN_FRONTEND='noninteractive' \
--pkg-manager apt \
--install opts="--quiet" \
gcc \
g++ \
octave \
--spm12 \
version=r7771 \
--freesurfer \
version=7.1.1 \
--copy $conda_yml_file /tmp/ \
--miniconda \
version=latest \
yaml_file=/tmp/$conda_yml_file \
env_name="csp" \
--env LD_LIBRARY_PATH="/opt/miniconda-latest/envs/csp:$LD_LIBRARY_PATH" \
--run-bash "source activate csp" \
--user csp \
--run 'mkdir /home/csp/data && chmod 777 /home/csp/data && chmod a+s /home/csp/data' \
--run 'mkdir /home/csp/output && chmod 777 /home/csp/output && chmod a+s /home/csp/output' \
--run 'mkdir /home/csp/code && chmod 777 /home/csp/code && chmod a+s /home/csp/code' \
--run 'mkdir /home/csp/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > home/csp/.jupyter/jupyter_notebook_config.py'
} |
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3rd note: After checking the differences in Dockerfile when executing the old script with - && sync \
- && sed -i '$isource activate csp' $ND_ENTRYPOINTWhy is |
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@kaczmarj : I found a workaround for now by using Example (make sure that generate_docker() {
docker run -i --rm repronim/neurodocker:0.9.4 generate docker \
--base-image neurodebian:stretch-non-free \
--yes \
--pkg-manager apt \
--install opts="--quiet" \
gcc \
g++ \
octave \
--spm12 \
version=r7771 \
--freesurfer \
version=7.1.1 \
--copy $conda_yml_file /tmp/ \
--miniconda \
version=latest \
yaml_file=/tmp/$conda_yml_file \
env_name=csp \
--user csp \
--run 'mkdir /home/csp/data && chmod 777 /home/csp/data && chmod a+s /home/csp/data' \
--run 'mkdir /home/csp/output && chmod 777 /home/csp/output && chmod a+s /home/csp/output' \
--run 'mkdir /home/csp/code && chmod 777 /home/csp/code && chmod a+s /home/csp/code' \
--run 'mkdir /home/csp/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > home/csp/.jupyter/jupyter_notebook_config.py' \
--workdir /home/csp/code \
--run 'echo source activate csp >> /home/csp/.bashrc'
}
I will close #16 in our repository for now (though you might find useful links there). I currently just follow this stackoverflow post by user merv who in general seems to know a lot of stuff about conda/Docker (helped me already a couple of times in the past on SO). General takeaways:
A possible solution for this issue: Reintroduce |
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we could bring it back but there are some sharp edges. we would have to test that we are activating the environment correctly. the |
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I guess the only way to achieve this to either hardcode it to some configuration file like I already tried the first approach which I find more elegant but somehow this doesn't work:
Using an ENTRYPOINT would also mean that you cannot use it for something else then. Afaik there can only be one ENTRYPOINT for each Dockerfile. |
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Note: One advantage of using an entrypoint would be that the conda environment could then also be used when you use |
This can be solved by adding #!/bin/bash
#. . . Do whatever you want here . . .
# we want the container to keep running after running the code above so we run this
/usr/bin/env bash |
This is happening because |
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This issue is stale because it has been open for 30 days with no activity. |
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This issue was closed because it has been inactive for 14 days since being marked as stale. |
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This issue is stale because it has been open for 30 days with no activity. |
We would like to create a new conda environment using a
.ymlfile. With our current script we end up with a container, where neither the base nor our custom "yml"-environment seem to be activated. E.g.:In old neurodocker versions, there was the
activate=Trueoption. I always thought this option did exactly that (activating a custom environment). On top of that, I could come up with a script (very close to an old version of generate_docker.sh from the nipype_tutorial) that uses 1.)activate=Trueand 2.)--env LD_LIBRARY_PATH="/opt/miniconda-latest/envs/csp:$LD_LIBRARY_PATH"and 3.)--run-bash "source activate csp". Here the activation seem to have worked (I am just not sure which of the three options / or their combination is responsible for that):Pasting both the old/new bash-scripts/Dockerfiles here:
Latest script:
Note that a
.ymlfile has to be present in the directory that the script is in. You can execute this script by runningbash generate_dockerfile.sh test_env.yml. For example usetest_env.ymlas provided in our repoLatest Dockerfile:
Old script uses
kaczmarj/neurodocker:0.7.0:Old Dockerfile:
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