Deploying the suffix array

Deploy using the CLI

Deploy using Docker

Deploy using the Unipept server

Exporting all variables

Many commands expect some environment variables to be set. By executing the following code in your terminal, you can set all required variables. Make sure these variables are updated before executing them.

# Absolute path to the virtual organisation on the HPC
export HPC_VO="/kyukon/data/gent/vo/000/gvo00038"
# Absolute path to the suffix array binary on the HPC
export SA_FILE="${HPC_VO}/suffix-array/sa_sparse3_compressed.bin"
# Current Uniprot release
export UNIPROT_VERSION="2024-03"
# Absolute path to the suffix array on the Unipept server
export INDEX_DIRECTORY="/mnt/data/uniprot-${UNIPROT_VERSION}"

Moving files from the HPC virtual organisation

Move the suffix array binary

scp "hpc-tibo:${SA_FILE}" "${INDEX_DIRECTORY}/suffix-array"

Deploying the suffix array

TODO

Creating the database

TODO