BIRCH
Local BLAST Databases
  Deleting BLAST Databases

April  5, 2017


Databases can be added to your local BLAST database directory from BIRCH Administration Tool, which can be launched from the BIRCH launcher using File --> birchadmin, or from the command line by typing 'birchadmin'.

In birchadmin, choose UpdateAddInstall --> Delete files from Blast Database.

1) Choose databases to delete
This menu lets you choose which databases to delete. A  [+] or [-] indicates, respectively, whether a database is already installed, or not. By default, all databases are de-selected, indicated by "Do nothing." To include a database in the list of databases to delete, choose Delete. If you select a database that is not listed as present, no action will be taken for that database.

Note that the databases are organized in to four tabs for Nucleotide, Protein, High-throughput or Other databases. Most of the "High-throughput" databases are nucleic sequences from high-throughput projects, such as ESTs, sequence-tagged sites. The one exception at this writing is Environmental - Protein. The other tab lists non-sequence databases, such as the taxonomy database, TaxDB. This is a small database, and includes taxonomy information needed for BLAST to identify species in BLAST reports, so it is probably useful to install this database.

3) Launch the job
Generally, deleting databases should be a very quick operation. To begin the selected databases, click on Run. The job will run in the background, meaning that you can quit BioLegato and logout if you wish during the download. If your system is configured to send email, you will receive a log of download progress by email, once all downloads are complete. The email will be sent to the BIRCH Administrator's email address, which was set when BIRCH was installed, and also appears on the BIRCH home page of your local copy of the documentation.
 
Note:  The [+]/[-] indicators in the Delete menu will not be updated to reflect deletion selected databases until the next time you launch birchadmin after the deletion is completed.


At the command line - Suppose you wanted to delete the Swissprot/Uniprot, vector and Taxonomy databases:

blastdbkit.py --delete --dblist swissprot,vector,taxdb

To delete all databases:

blastdbkit --delete --dblist all
For obvious reasons, this is potentially a dangerous option!


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