Make
The three platform-specific makefiles
Makefile.Cygwin,
Makefile.Linux,
and
Makefile.MacOSX
handles the small differences in operating systems.
The generic Makefile
Makefile.generic,
which is included by the three platform-specific makefiles,
does the bulk of the work.
The file
Makefile.generic
consists of several sections:
-
Top Section:
This section defines macros for groups of files
and dependencies for executables.
In particular,
-
make all compiles all programs,
-
make clean removes temporary files,
-
make clobber removes compiled executables,
-
make spotless removes results files.
-
PseudoBase:
This section provides rules to extract RNA data from
pseudobase.fasta,
to split the data into RNA sequence and dot-brackets
in seq and db formats,
and to convert the dot-brackets to base pairs and helices
in pkb.bp and pkb.hx formats.
It also contains a target pkb for the preparation of experiments.
-
HotKnot:
This section provides rules to convert the bpseq files
precomputed by HotKnot to
hotknot.bp and hotknot.hx formats,
and a target hot for the preparation of experiments.
Note that this section also contains rules
to compute RNA secondary structures using HotKnot,
but these rules are commented out because HotKnot works on Linux only.
-
Delta:
This section provides rules to use our folding simulation program
and 3D visualization program on individual sequences.
Note in particular the three targets
result, show, and movie
discussed in Download and Install Software.
-
Experiments and Analysis:
This section includes all the scripts for automating experiments
and analysis.
Note in particular the targets
delta, stop,
txt,
scr,
scatter.pdf,
and
reconstruct
discussed in Repeat Experiments.
-
Software Package:
This section provides rules for two targets:
all.zip is an archive of the complete software package;
code.pdf is a single-pdf printout of the complete source code.
The file
Makefile.generic
contains many shortcuts for typical tasks.
For example,
-
make PKB00001.seq
extracts the sequence PKB00001.seq from pseudobase.fasta.
-
make PKB00001.delta.bp
uses the folding simulation program to predict base pairs
for the sequence PKB00001.seq.
-
make PKB00001.delta.hx
converts the base pairs to helices.
-
make PKB00001.delta.hx2i
converts helices to 2-intervals in textual format.
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