pull entire database (not counts) and save to output_dir for archival purposes
archiveDatabase.Rdsaves both the individual tables, including counts, and the combined_df
Usage
archiveDatabase(
database_host,
database_name,
database_user,
database_password,
output_dir,
archive_counts_flag = TRUE
)Arguments
- database_host
if connecting to a database hosted on AWS, it might be something like ec2-54-83-201-96.compute-1.amazonaws.com
- database_name
name of the database, eg for cryptococcus kn99, the database might be named kn99_database. Check with the documentation, whoever set up the database, or get into the server and check directly
- database_user
a user of the actual database, with some level of permissions. You'll need to check with the database maintainer for this. It is suggested that you use a .Renviron file in your local project (make sure it is completely ignored by git, R, etc) to store this info
- database_password
password to the database user. You'll need to check with the database maintainer for this. It is suggested that you use a .Renviron file in your local project (make sure it is completely ignored by git, R, etc) to store this info
- output_dir
where to deposit a subdirectory, named by todays date in this format: 20210407, with the tables and combined_df inside. eg a mounted local directory /mnt/htcf_lts/crypto_database_archive/ --> /lts/mblab/Crypto/rnaseq_data/crypto_database_archive
- archive_counts_flag
boolean indicating whether or not to save the counts. default is TRUE