BeeDeeM configuration

BeeDeeM installation directory

Whatever the installation used, BeeDeeM is located within a directory, hereafter calle ${installDir}.

The BeeDeeM directory ${installDir} is organised as follows (Linux/OSX defaults):

Directory	Content	Default value
${installDir}	Home directory of BeeDeeM	/opt/beedeem (1)
${installDir}/bin	Java libraries for BeeDeeM and its dependencies	${installDir}/bin
${installDir}/external	Native binaries (such as makeblastdb) for Linux, MacOSX or Windows	${installDir}/external
${descriptors}	Directory containing particular files called: databank descriptor files. These files instruct the software how to install databanks.	${installDir}/conf/descriptors
${scripts)	Databank descriptors additional pre- and post-processing tasks	${installDir}/conf/scripts

(1) Default values for Legacy, Docker or Singularity installation ; Conda may use a different path.

BeeDeeM additional directories

Directory	Description	Default value
${biobaseRootDir}	The place where all banks are installed. Inside that directory, BeeDeeM creates and manages sub-directories.	See "Master configuration file", below
${workingDir}	Used by BeeDeeM to create log files, temporary files, etc.	See "Working directory", below

Master configuration file

By default, BeeDeeM is configured by a master configuration file located in ${installDir}/conf: dbms.config. Content of this file is setup during software installation. This text file contents a set of key/value pairs and is documented, so quite easy to understand.

Actually, there is a single very important key/value to look at : mirror.path. That key defines the path to ${biobaseRootDir}. +

You have three options to (re)define the value associated to that key:

• by editing dbms.config; suitable for legacy installation, it is more difficult to use that solution for any other installations of BeeDeeM, i.e. Conda, Docker or Singularity;

• by setting JRE argument KL_mirror.path(1); e.g. by editing bdm master command-line script and setting: java .../... -DKL_mirror.path=/a/new/path/to/bank/repository

• by setting KL_mirror__path (2) environment variable; e.g. for bash shell: export KL_mirror__path=/a/new/path/to/bank/repository

(1) variable names are case sensitive; (2) there are indeed two underscore characters between "mirror" and "path", this is NOT a typo.

The latter solution is realy the most recommended one to use with Conda, Docker or Singularity installation of BeeDeeM.

It is worth noting that environment variable declaration takes priority over JRE -D declaration that takes priority over dbms.config file declaration.

Working directory

BeeDeeM relies on a dedicated directory to store all its working files: log files, temporary files, etc. By default, that directory is set within bdm master command script file (located in ${installDir}) by variable: KL_WORKING_DIR.

You can change the location of that directory at any time using the following declaration (bash shell) before starting BeeDeeM:

export KL_WORKING_DIR=/a/new/path/to/workdir.

Additional configuration controls

Additional KL_ prefixed variable names exist to easity setup BeeDeeM. As for KL_mirror__path and KL_WORKING_DIR, these additional KL_ variables can be setup using one of:

• export KL_XXX=a_value

• java .../... -DKL_XXX=a_value

And again, shell variable declaration takes priority over JRE -D declaration.

Log file

The following variables control the creation of BeeDeeM log files:

Variable	Role	Default
KL_LOG_TYPE	one of: none, console or file	file
KL_LOG_FILE	name of log file	If not set, BeeDeeM creates a log file using sub-command name
KL_DEBUG	one of: true or false	false

Configuration directory

By default, BeeDeeM locates bank descriptors in ${descriptors} (see above). In case you would like to use your own configuration directory (e.g. containing new bank descriptors), you can tell BeeDeeM to use that directory as follows:

KL_CONF_DIR=/path/to/new/conf_dir

Such a path must target all expected configuration sub-directories: system, scripts, descriptors. The very easy way to achieve that consists in copying the standard BeeDeeM "conf" directory, then update that copy to meet your needs.