Databank descriptors

What is a databank descriptor ?

A databank descriptor is a text file containing the instructions used by BeeDeeM to download and install databanks.

There are two types of descriptor:

• bank descriptor (.dsc file): descriptor used to describe the installation of a single databank

• global descriptor (.gd file): descriptor used to start the installation of one or several databanks

Description of databases to be managed: the bank descriptor

By default, BeeDeeM provides a non-exhaustive list of descriptors for processing various sequence databanks and biological classifications (ontologies). All of these files are suffixed with extension “.dsc” and are located in ${conf} directory.

Each file contains a group of instructions used by BeeDeeM:

• to download (via FTP) all files making up the complete distribution of a database

• to process the downloaded files to make them usable (decompressing, un-archiving, indexing, etc.)

Here is a sample bank descriptor aims at installing Uniprot_SwissProt:

# Bank name
db.name=Uniprot_SwissProt
# Bank description
db.desc=UniprotKB/SwissProt databank (contains annotations).
# Bank type
db.type=p
# Bank location
db.ldir=${mirrordir}|p|Uniprot_SwissProt

# Server access
ftp.server=ftp.expasy.org
ftp.port=21
ftp.uname=anonymous
ftp.pswd=[e-mail]
# Directory to locate files to download
ftp.rdir=/databases/uniprot/current_release/knowledgebase/complete
ftp.rdir.exclude=

# File(s) to retrieve
db.files.include=uniprot_sprot.dat.gz
db.files.exclude=

# Processing tasks
tasks.unit.post=gunzip,idxsw
tasks.global.post=delgz,deltmpidx,formatdb(lclid=false;check=true;nr=true)

# Keep previous release or not
history=0

The use of such a file will be explained in the next section.

The full format of the database descriptors is documented in section Databank descriptor format.

Description of processing to be performed: the global descriptor

The processing that BeeDeeM will perform is described in a global descriptor.

Here is an example of such a descriptor:

# List of banks to retrieve (use bank descriptor name)
db.list=PDB_protein

# What to do (download or info)
db.main.task=download

# Restart a failed process
resume.date=none

# Parameters of the loader engine
task.delay=1000
ftp.delay=5000
ftp.retry=3

# Do we have to send an email to DBMS manager?
mail.smtp.host=
mail.smtp.port=
mail.smtp.sender.mail=
mail.smtp.sender.pswd=
mail.smtp.recipient.mail=

By default, BeeDeeM has a “test” descriptor for processing the installation of PDB Protein.

This descriptor is the file named 'test.gd' located in the directory ${conf}.

Note: We will use this file 'test.gd' in the rest of this manual to explain how to use BeeDeeM. However, you can create other descriptors (e.g. by deriving them from 'test.gd'), but always be sure to save them in the directory ${conf}.

Before starting any processing, it is VERY IMPORTANT to check the following two lines in the global descriptor:

db.list=PDB_Protein
resume.date=none

The first line is a comma separated list of database descriptors to use (without their ".dsc" extension). It defines which databank(s) will be installed during a single BeeDeeM processing.

The second line gives a restart date. This line is only used in the case of a restart after a failure. If you start BeeDeeM for the first time or if you are updating the databases, it is absolutely imperative to set "resume.date" to the value none. All of this is explained in section Advanced uses.

But now, let's see how to install a databank using these descriptors!