Stacks

Widely-used Radseq analysis software protocol by Julian Catchen.

Steps

• Create database, you must have the appropriate privileges for this. If you do, the command will be something like:

echo "CREATE DATABASE <mynewdbname>" | mysql -h <name_of_server_running_mysql> -u <myusername> -p

• Ensure $STACKSROOTDIR/share/stacks/sql/my.cnf is set up properly

• Ensure modification privileges for the user

• Load stack.sql schema onto the database. It's in $STACKSROOTDIR/share/stacks/sql/stacks.sql, i.e.

mysql <mydbname> -h <name_of_server_running_mysql> -u <myusername> -p < $STACKSROOTDIR/share/stacks/sql/stacks.sql

• For whatever reason one can also start over by deleting a database. Care should be taken with a step like this, just in case one deletes the wrong database. The delete command's keyword is in fact "DROP" and woudl be run like this:

echo "DROP DATABASE <mynewdbname>" | mysql -h <name_of_server_running_mysql> -u <myusername> -p