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 descriptionbdm install -h
: display usage of toolinstall
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}.
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