BeeDeeM reference manual

BeeDeeM master command

Running BeeDeeM is as simple as using the unique command: bdm.

You get help with: bdm -h or bdm --help.

Expected first argument of bdm command is one of the following sub-commands (also called BeeDeeM tools):

sub-command	description
annot	annotate a BLAST XML formatted file
check	check whether or not a descriptor is still ok (URL not broken, etc)
delete	delete bank(s)
desc	get list of bank descriptors from default conf directory, i.e. ${installDir}/conf/descriptors
info	print out list of installed banks
install	install bank(s)
query	query bank repository to fetch entry(ies) given ID(s)
ui	start bank manager graphical user interface

You can easily get an overview of all these tools using such a command:

• bdm -h: display available list of tools along with a short description

• bdm install -h: display usage of tool install

Note: during BeeDeeM execution, there is nothing displayed on the terminal whether something goes OK or wrong. However, BeeDeeM logs all its work in a dedicated log file located in ${workingDir}.