- Place pre-formatted databases in the directory selected as BLAST database location on the server file system. The CLC Server will automatically detect the database files and list the database as target when running BLAST. You can download pre-formatted database from e.g. ftp://ftp.ncbi.nih.gov/blast/db/.
- Run the Create BLAST Database () tool via your Workbench, and choose to run the function on the Server when offered the option in the Workbench Wizard. You will get a list of the BLAST database locations that are configured on your Server. The final window of the wizard offers you a location to save the output to. The output referred to is the log file for the BLAST database creation. The BLAST databases themselves are stored in the designated BLAST database folder you chose earlier in the setup process.
A note on permissions: To create BLAST databases on the Server, using the Workbench interface, the user running the CLC Server process must have file system level write permission on the import/export directory that you have configured to hold BLAST database.
By default, if you do not change any permissions within CLC Server, all users logging into the CLC Server (e.g., via their Workbench, or via the Command Line Tools), will be able to create BLAST databases in the areas you have configured to hold BLAST databases.
If you wish to restrict the ability to create BLAST databases to these areas completely, but still wish your users to be able to access the BLAST databases to search against, then set the file system level permissions on the import/export directory so they are read-only.
When listing the databases as shown in figure 11.2, it is possible to delete the databases by clicking the Delete link at the far right-hand side of the database information.