Directory structure
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Basically, BeeDeeM expects to access two directories for processing banks installation at runtime:
a working directory (workingDir): to create log files, temporary files, etc.
a bank home directory (biobaseRootDir): the place where all banks are installed. Inside that directory, BeeDeeM creates and manages sub-directories... you are invited to avoid editing manually that structure!
Note: when using the legacy or Conda installer, there is a third directory, refer to as installDir, where BeeDeeM software has been installed. More on this in the next section.
Of course, BeeDeeM requires read/write permissions on workingDir and biobaseRootDir directories.
When using the legacy installer, workingDir and biobaseRootDir are set at installation time.
When using either Docker, Singularity or Conda installation mode, workingDir and biobaseRootDir are set at runtime using KL_WORKING_DIR and KL_mirror__path environment variables, respectively (variable names are case sensitive and there are indeed two underscore characters between "mirror" and "path", this is NOT a typo; more on this later).