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uta_installation.md

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  1. Switch to your admin account #Skip if your user already has sudo permissions
    1. su wag002adm # replace with your admin account name
  2. Start postgres
    1. pg_ctl -D /opt/homebrew/var/postgres start
    2. ps aux | grep postgres #to make sure that this process is running
  3. Start psql and open database postgres, which is the database postgres uses itself to store roles, permissions, and structure:
    1. psql postgres
  4. Create roles for the application, give login and CREATEDB permissions:
    1. CREATE ROLE uta_admin WITH LOGIN CREATEDB;
    2. CREATE ROLE anonymous WITH LOGIN CREATEDB;
  5. List the users using the command
    1. \du
  6. Create the UTA Database object
    1. CREATE DATABASE uta;
  7. Grant privileges to manage the database to uta_admin
    1. GRANT ALL PRIVILEGES ON DATABASE uta TO uta_admin;
  8. Exit postgres
    1. \q
  9. Download the UTA database and place it in the uta database object that you created before (This step takes around 5 hours).
    1. export UTA_VERSION=uta_20241220.pgd.gz\ncurl -O http://dl.biocommons.org/uta/$UTA_VERSION\ngzip -cdq ${UTA_VERSION} | psql -h localhost -U uta_admin --echo-errors --single-transaction -v ON_ERROR_STOP=1 -d uta -p 5432
  10. Set your UTA path
    1. export UTA_DB_URL=postgresql://uta_admin@localhost:5432/uta/uta_20241220 ###Optional installation step
  11. If you wanted to wait for the 5 hour update till later please follow these steps instead:
  12. Download the UTA database and place it in the uta database object that you created before.
    1. export UTA_VERSION=uta_20241220.pgd.gz curl -O http://dl.biocommons.org/uta/$UTA_VERSION gzip -cdq ${UTA_VERSION} | grep -v "^REFRESH MATERIALIZED VIEW" | psql -h localhost -U uta_admin --echo-errors --single-transaction -v ON_ERROR_STOP=1 -d uta -p 5432
  13. Run the refresh materialized view commands
    1. REFRESH MATERIALIZED VIEW uta_20241220.exon_set_exons_fp_mv;
    2. REFRESH MATERIALIZED VIEW uta_20241220.tx_exon_set_summary_mv;
    3. REFRESH MATERIALIZED VIEW uta_20241220.tx_def_summary_mv;
    4. REFRESH MATERIALIZED VIEW uta_20241220.tx_similarity_mv; #This step will take 5 or more hours