Quick start guide

In this section we present the use of BeeDeeM command-line tools whatever the installation you use (legacy, Docker, Singularity or Conda).

So, when we say: "use bdm tool to do something", you will have to adapt the command-line to conform to your installation. Examples:

• Legacy and Conda installations: you can invoke BeeDeeM tools directly, since path to BeeDeeM tools is added in your PATH environment variable

• Docker: prefix BeeDeeM command-line tool name with: "docker run .../..."

• Singularity: prefix BeeDeeM command-line tool name with: "singularity run .../..."

BeeDeeM master command

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

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

BeeDeeM sub-commands

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