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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 and /pre/data already exist. If it succeeds, it will create /pre/data/run and put output there.

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