PRE is an input directory necessary for running Arachne. The PRE directory is a root directory for all project work performed by Arachne; the directories DATA, RUN, SUBDIR, and OUTDIR are all subdirectories of PRE at some level. You can set a default value for PRE by setting the ARACHNE_PRE environment variable, in which case you will not need to set PRE at the command line.
Note that PRE must be an absolute directory location (i.e., beginning with a backslash). It cannot be relative, and it cannot begin with a tilde (~) indicating a home directory. The PRE directory must also contain certain files and subdirectories that Arachne needs; see Input for details.
For example, the script Assemblez requires the following command-line form:
Assemblez PRE=/pre DATA=data RUN=run
This will fail unless the directories
/pre/data already exist. If it succeeds, it will create
/pre/data/run and put output there.