/PRE/ DATA/ fasta/ qual/ traceinfo/ RUN/ work/ SUBDIR/ OUTDIR/ KEY/ dtds/ vector/ e_coli/ e_coli_transposons/
The directories PRE, DATA, RUN, SUBDIR, OUTDIR, and KEY have variable names. A singular assembly (or a step in the assembly process) is uniquely identified by choosing some of these directories and specifying them as command-line arguments to Arachne modules. PRE is a full path name (i.e., it begins with a backslash), while all others are specified relative to their immediate parents in the directory tree. (Note that relative directories may contain more than one level; RUN is not necessarily an immediate subdirectory of DATA.)
The other directories mentioned above have constant names, and must be set up by the user as input.
Arachne code base
ARACHNE_DIR, like PRE, is a full path name. ARACHNE_BIN_DIR, when specified as an environment variable, is relative to ARACHNE_DIR.