Conda env does not activate at start even if activate=true

I’m unable to get my conda env to activate by default with --miniconda activate=True and need to manually enter source activate neuro upon starting the singularity container with singularity shell . I’d like to run the container from a bash/slurm script and it will not allow me to activate the env.

@satra was helping to look into this and this does work on a docker image based on ubuntu

Apparently the line sed -i '$isource activate neuro' $ND_ENTRYPOINT is not executing

Neurodocker command: singularity run neurodocker.simg generate singularity --base centos:7 --pkg-manager yum --user neuro --miniconda create_env=neuro activate=True conda_install="numpy pandas scipy scikit-learn matplotlib seaborn networkx ipython joblib nibabel datalad jupyter numba" pip_install="nibabel ply neurosynth nilearn pliers kmapper dyneusr pyns umap-learn librosa pydra tensorflow pysoundfile resampy" --install emacs vim --run "python -m pip install git+https://github.com/nipype/pydra-ml.git" > Singularity

Build Spec:

# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
# Latest release: Neurodocker version 0.7.0
# Timestamp: 2020/05/22 20:04:12 UTC
# 
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
# pull request on our GitHub repository:
# 
#     https://github.com/ReproNim/neurodocker

Bootstrap: docker
From: centos:7

%post
su - root

export ND_ENTRYPOINT="/neurodocker/startup.sh"
yum install -y -q \
    bzip2 \
    ca-certificates \
    curl \
    localedef \
    unzip
yum clean packages
rm -rf /var/cache/yum/*
localedef -i en_US -f UTF-8 en_US.UTF-8
chmod 777 /opt && chmod a+s /opt
mkdir -p /neurodocker
if [ ! -f "$ND_ENTRYPOINT" ]; then
  echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT"
  echo 'set -e' >> "$ND_ENTRYPOINT"
  echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT"
  echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT";
fi
chmod -R 777 /neurodocker && chmod a+s /neurodocker

test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
su - neuro

export PATH="/opt/miniconda-latest/bin:$PATH"
echo "Downloading Miniconda installer ..."
conda_installer="/tmp/miniconda.sh"
curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash "$conda_installer" -b -p /opt/miniconda-latest
rm -f "$conda_installer"
conda update -yq -nbase conda
conda config --system --prepend channels conda-forge
conda config --system --set auto_update_conda false
conda config --system --set show_channel_urls true
sync && conda clean -y --all && sync
conda create -y -q --name neuro
conda install -y -q --name neuro \
    "numpy" \
    "pandas" \
    "scipy" \
    "scikit-learn" \
    "matplotlib" \
    "seaborn" \
    "networkx" \
    "ipython" \
    "joblib" \
    "nibabel" \
    "datalad" \
    "jupyter" \
    "numba"
sync && conda clean -y --all && sync
bash -c "source activate neuro
  pip install --no-cache-dir  \
      "nibabel" \
      "ply" \
      "neurosynth" \
      "nilearn" \
      "pliers" \
      "kmapper" \
      "dyneusr" \
      "pyns" \
      "umap-learn" \
      "librosa" \
      "pydra" \
      "tensorflow" \
      "pysoundfile" \
      "resampy""
rm -rf ~/.cache/pip/*
sync
sed -i '$isource activate neuro' $ND_ENTRYPOINT


yum install -y None \
    emacs \
    vim
yum clean packages
rm -rf /var/cache/yum/*

python -m pip install git+https://github.com/nipype/pydra-ml.git

echo '{
\n  "pkg_manager": "yum",
\n  "instructions": [
\n    [
\n      "base",
\n      "centos:7"
\n    ],
\n    [
\n      "user",
\n      "root"
\n    ],
\n    [
\n      "_header",
\n      {
\n        "version": "generic",
\n        "method": "custom"
\n      }
\n    ],
\n    [
\n      "user",
\n      "neuro"
\n    ],
\n    [
\n      "miniconda",
\n      {
\n        "create_env": "neuro",
\n        "activate": true,
\n        "conda_install": [
\n          "numpy",
\n          "pandas",
\n          "scipy",
\n          "scikit-learn",
\n          "matplotlib",
\n          "seaborn",
\n          "networkx",
\n          "ipython",
\n          "joblib",
\n          "nibabel",
\n          "datalad",
\n          "jupyter",
\n          "numba"
\n        ],
\n        "pip_install": [
\n          "nibabel",
\n          "ply",
\n          "neurosynth",
\n          "nilearn",
\n          "pliers",
\n          "kmapper",
\n          "dyneusr",
\n          "pyns",
\n          "umap-learn",
\n          "librosa",
\n          "pydra",
\n          "tensorflow",
\n          "pysoundfile",
\n          "resampy"
\n        ]
\n      }
\n    ],
\n    [
\n      "install",
\n      [
\n        "emacs",
\n        "vim"
\n      ]
\n    ],
\n    [
\n      "run",
\n      "python -m pip install git+https://github.com/nipype/pydra-ml.git"
\n    ]
\n  ]
\n}' > /neurodocker/neurodocker_specs.json

%environment
export LANG="en_US.UTF-8"
export LC_ALL="en_US.UTF-8"
export ND_ENTRYPOINT="/neurodocker/startup.sh"
export CONDA_DIR="/opt/miniconda-latest"
export PATH="/opt/miniconda-latest/bin:$PATH"

%runscript
/neurodocker/startup.sh "$@"

[kaczmarj]

@djarecka - i don’t think so. i do not have time right now to work on this.

[djarecka]

@kaczmarj - thanks, I’ll give a try