install_easybuild.sh

#!/usr/bin/env bash

### EasyBuild Installation and Module Deployment

##################################################################
## Make lmod available
##################################################################

source /usr/share/lmod/lmod/init/bash

###################################################################
### Deploy modules - Environmental Variables

export EASYBUILD_PREFIX=/apps/easybuild/1.0
export MODULEPATH=/apps/easybuild/1.0/modules/all
export ROBOT=/app/software-configs
export ANACONDA3_BASE="$HOME/.local/anaconda3"
export EB_ENV=eb-4.0.0
export PATH=${ANACONDA3_BASE}/bin:$PATH
export PATH="${ANACONDA3_BASE}/envs/${EB_ENV}/bin/:$PATH"

function install_miniconda {
        curl -s -L https://repo.continuum.io/miniconda/Miniconda3-py38_4.8.2-Linux-x86_64.sh > miniconda.sh

        chmod 777 miniconda.sh ; bash miniconda.sh -f -b -p $ANACONDA3_BASE
        rm miniconda.sh && \
            export PATH=${ANACONDA3_BASE}/bin:$PATH && \
            conda config --set show_channel_urls True && \
            conda config --add channels conda-forge && \
            conda config --add channels bioconda && \
            conda config --set always_yes True && \
            conda update --all --yes && \
            conda config --set allow_softlinks False && \
            conda clean -tipy
}

function install_easybuild {
        ##################################################################
        ## Add Easybuild Config
        ## This is just a placeholder, but needed for some setups
        ##################################################################
        mkdir -p $HOME/.config/easybuild

        ##################################################################
        ## Install Easybuild and Lmod
        ## Create a conda env with easybuild
        ## Then update the easybuild env with pip to get the 4.0.0 version
        ##################################################################
        FILE="eb-env-${EB_ENV}.yml"

cat <<EOM >$FILE
# Install easybuild from an env file
name: ${EB_ENV}
channels:
  - conda-forge
  - defaults
dependencies:
  - python=2.7
  - jinja2
  - pip
  - anaconda-client
  - pip:                            # Packages installed from PyPI
    - easybuild==4.0.0
EOM
        conda env create -f $FILE
        T_PWD=$PWD
        cd /tmp
        wget https://raw.githubusercontent.com/jerowe/easybuild-easyblocks/develop/easybuild/easyblocks/generic/conda.py
        find ${ANACONDA3_BASE}/envs/${EB_ENV} -type f -name conda.py | grep generic | xargs -I {} mv /tmp/conda.py {}
        cd $T_PWD
        ##################################################################
        ## Install an Easybuild Config
        ## Miniconda3 is a Core EB config
        ## --software-name is a way of telling EB to look for software
        ## from the repos instead of supplying a .eb file
        ##################################################################
        # This times out if it's done from the initialization script
        # Just run it manually
        source activate $EB_ENV && \
                eb --software-name Miniconda3
}

##################################################################
## Anaconda Setup
## We are using miniconda3/python3 from anaconda
## Be sure to change this if you are running as a your own user
##################################################################

if [ ! -d "${ANACONDA3_BASE}" ]; then
  echo "No anaconda3 found. Installing..."
  install_miniconda
else
  echo "Anaconda3 installation already present. Exiting."
fi

if [ ! -d "${ANACONDA3_BASE}/envs/${EB_ENV}" ]; then
  echo "No easybuild found. Installing..."
 install_easybuild
else
  echo "EasyBuild installation already present. Exiting."
fi