install_cryosparc_master.sh

#!/bin/bash

source set_environment.sh

# Check that SPARCDIR is provided where cryoSPARC will be installed
if [ -z ${SPARCDIR+x} ]
then
    echo "SPARCDIR not set, quitting"
    exit
fi

mkdir -p ${SPARCDIR}
cd ${SPARCDIR}

# Check that license is provided
if [ -z ${LICENSE_ID+x} ]
then
    echo "Provide a valid LICENSE_ID before downloading"
    exit
fi

# Download and extract tar files
curl -L https://get.cryosparc.com/download/master-latest/$LICENSE_ID -o cryosparc_master.tar.gz
tar -xf cryosparc_master.tar.gz

# Install master
if [ ! -d ${SPARCDIR}/cryosparc_master ]; then
    echo "Installation files not found! Exiting"
    exit
fi
cd ${SPARCDIR}/cryosparc_master
user_id=$(whoami)
export port_number=${user_id: -4}0
export master_hostname=$(echo -e "$(hostname -f)" | tr -d '[:space:]')

./install.sh --license $LICENSE_ID \
             --hostname ${master_hostname} \
             --dbpath ${SPARCDIR}/db \
             --port ${port_number}

# There is a bug where jobs cannot be submitted from cryoSPARC, because it
# sets LD_PRELOAD to its own Python library, which causes problems when
# submitting a job because the system Python has another version and its
# packages cannot be found. The temporary workaround is to link required
# Python packages (slurm_foz) in the cryoSPARC conda environment
ln -s /usr/lib/python3.6/site-packages/slurm_foz \
    ${SPARCDIR}/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.8/site-packages/