Directory tree

From ArachneWiki

The directory tree of an assembly project is the structure containing all of its input and output files.

/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

A separate directory tree will contain the Arachne code package. The root directory of this tree is ARACHNE_DIR, which comes directly out of the tarball when you download Arachne.

/ARACHNE_DIR/
             ARACHNE_BIN_DIR/

ARACHNE_DIR, like PRE, is a full path name. ARACHNE_BIN_DIR, when specified as an environment variable, is relative to ARACHNE_DIR.