BIRCH - Installing and configuring BLAST Databases

Local BLAST Databases
Configuration

April 25, 2016

In most cases, you don't need to do anything to configure BIRCH to use a local copy of NCBI databases.

When you first install BIRCH, or update an existing BIRCH installation, the getbirch scripts will check to see if the $BLASTDB environment variable is already set, indicating the location of previously-installed BLAST databases. The BLASTDB directory will be scanned to find database files, and BioLegato menus will be updated to show these databases as being installed. If $BLASTDB is not set, the location of your BLAST database will default to $BIRCH/GenBank.

Changing the location of the BLASTDB directory

If you wish to download database files to a different directory, you can change the $BLASTDB environment variable in birchadmin using UpdateAddInstall --> BLASTDB - Choose BLAST database directory.

All this does is to run blastdbkit.py --configure, which will change $BLASTDB, and the new directory will be scanned to locate BLAST databases.

Alternative: Instead of changing BLASTDB to point to a different directory, an alternative approach would be to
replace the $BIRCH/GenBank directory with a symbolic link to your own BLASTDB directory. For example, if you already had a copy of BLAST databases in the directory '/workspace/NCBIBLAST', you could do the following:

cd $BIRCHrmdir GenBankln -s /workspace/NCBIBLAST GenBank

This way, $BLASTDB could have the value $BIRCH/GenBank, but filesystem references to this directory would be re-directed to /workspace/NCBIBLAST.

At the command line - Suppose you wanted to set the BLASTDB directory to /workspace/ BLAST

blastdbkit.py --configure --blastdb /workspace/BLAST

It is always safe to run UpdateAddInstall --> BLASTDB - Choose BLAST database directory.

If, for example, you had reason to believe that database files were present, but were not shown as installed in BioLegato menus, you could run this program to force blastdbkit.py to re-scan the $BLASTDB directory. This might also be a first step if you had accidentally deleted or overwritten some database files, run this program to ensure that BioLegato menus correctly reflected the files actually present. You could use BLASTDB - Add or BLASTDB - Install/Update to download and install the files that were deleted or damaged.

At the command line:

blastdbkit.py --configure

Setting up an email server for outgoing mail

In order to receive email notifications when installation of databases is complete, your computer must be running an email server that at the very least allows outgoing email. See BIRCH Administration - Email notification for instructions.

Please send suggestions of comments regarding this page to psgendb@cc.umanitoba.ca