conda: command not found

[mosoriob]

When the container starts, it doesn't find conda

environment: line 17: /opt/apps/lmod/lmod/libexec/lmod: No such file or directory
False
Checking if miniconda3 is installed...
Initializing conda...
no change     /work/07025/mosorio/ls6/miniconda3/condabin/conda
no change     /work/07025/mosorio/ls6/miniconda3/bin/conda
no change     /work/07025/mosorio/ls6/miniconda3/bin/conda-env
no change     /work/07025/mosorio/ls6/miniconda3/bin/activate
no change     /work/07025/mosorio/ls6/miniconda3/bin/deactivate
no change     /work/07025/mosorio/ls6/miniconda3/etc/profile.d/conda.sh
no change     /work/07025/mosorio/ls6/miniconda3/etc/fish/conf.d/conda.fish
no change     /work/07025/mosorio/ls6/miniconda3/shell/condabin/Conda.psm1
no change     /work/07025/mosorio/ls6/miniconda3/shell/condabin/conda-hook.ps1
no change     /work/07025/mosorio/ls6/miniconda3/lib/python3.11/site-packages/xontrib/conda.xsh
no change     /work/07025/mosorio/ls6/miniconda3/etc/profile.d/conda.csh
no change     /home1/07025/mosorio/.bashrc
No action taken.
/tapis/run.sh: line 43: conda: command not found
Sourcing .bashrc...
Installing Conda env
/tapis/run.sh: line 54: python: command not found

If you use conda from the jupyter notebook, you are using the conda installed on the node

Apptainer> env | grep -i conda
CONDA_EXE=/work/07025/mosorio/ls6/miniconda3/bin/conda
USER_PATH=/opt/apps/xalt/xalt/bin:/opt/apps/tacc-apptainer/1.1.8/bin:/work/07025/mosorio/ls6/miniconda3/condabin:/opt/apps/pmix/3.2.3/bin:/opt/apps/cmake/3.24.2/bin:/opt/apps/intel19/python3/3.9.7/bin:/opt/intel/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin:/opt/intel/compilers_and_libraries_2020.1.217/linux/bin/intel64:/opt/apps/gcc/9.4.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:.:/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/local/sbin
__LMOD_REF_COUNT_PATH=/opt/apps/xalt/xalt/bin:1;/opt/apps/tacc-apptainer/1.1.8/bin:1;/work/07025/mosorio/ls6/miniconda3/condabin:1;/opt/apps/pmix/3.2.3/bin:1;/opt/apps/cmake/3.24.2/bin:1;/opt/apps/intel19/python3/3.9.7/bin:2;/opt/intel/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin:1;/opt/intel/compilers_and_libraries_2020.1.217/linux/bin/intel64:1;/opt/apps/gcc/9.4.0/bin:1;/usr/local/bin:1;/usr/bin:1;/usr/local/sbin:1;/usr/sbin:1;.:1
_CE_CONDA=
CONDA_SHLVL=0
CONDA_PYTHON_EXE=/work/07025/mosorio/ls6/miniconda3/bin/python
Apptainer> env | grep -i conda
CONDA_EXE=/work/07025/mosorio/ls6/miniconda3/bin/conda
USER_PATH=/opt/apps/xalt/xalt/bin:/opt/apps/tacc-apptainer/1.1.8/bin:/work/07025/mosorio/ls6/miniconda3/condabin:/opt/apps/pmix/3.2.3/bin:/opt/apps/cmake/3.24.2/bin:/opt/apps/intel19/python3/3.9.7/bin:/opt/intel/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin:/opt/intel/compilers_and_libraries_2020.1.217/linux/bin/intel64:/opt/apps/gcc/9.4.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:.:/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/local/sbin
__LMOD_REF_COUNT_PATH=/opt/apps/xalt/xalt/bin:1;/opt/apps/tacc-apptainer/1.1.8/bin:1;/work/07025/mosorio/ls6/miniconda3/condabin:1;/opt/apps/pmix/3.2.3/bin:1;/opt/apps/cmake/3.24.2/bin:1;/opt/apps/intel19/python3/3.9.7/bin:2;/opt/intel/compilers_and_libraries_2020.4.304/linux/mpi/intel64/bin:1;/opt/intel/compilers_and_libraries_2020.1.217/linux/bin/intel64:1;/opt/apps/gcc/9.4.0/bin:1;/usr/local/bin:1;/usr/bin:1;/usr/local/sbin:1;/usr/sbin:1;.:1
_CE_CONDA=
CONDA_SHLVL=0

[wmobley]

Wait but in the run.sh
When it echos:
Checking if miniconda3 is installed...
and then
Initializing conda...

That means it found conda other wise:

echo "Checking if miniconda3 is installed..."
if [ ! -d "$WORK/miniconda3" ]; then
echo "Miniconda not found in $WORK..."
  echo "Installing..."

[mosoriob]

I plan to test the Miniconda Docker image approach.
https://github.com/ContinuumIO/docker-images/blob/main/miniconda3/debian/Dockerfile