Sfold Executable Code for Academic Users, Version 2.2
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License Terms
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The Sfold Executable Code for Academic Users is a software for 
statistical folding and rational design of nucleic acids. Use of this 
program is restricted to non-commercial internal research only. Please 
read the license agreement (located at 
./license/SFOLD-EXE-ACADEMIC.html from your extracted package OR
http://www.wadsworth.org/resnres/bioinfo/sfold/SFOLD-EXE-ACADEMIC.html
from the web) before using this program. For more information about 
our software, please visit us online at http://sfold.wadsworth.org/ .


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Requirements
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The Sfold Executable Code currently runs on Linux (i386/x86_64) 
and Mac OS X (i386).

To run the Sfold Executable Code, you will need to have the following
software and libraries installed in your system:
- The R Project for Statistical Computing (http://www.r-project.org/)
- Perl (http://www.perl.org/)

The Mac OS X binaries have the following additional requirements.
These requirements provide .dylib dynamically-loaded libraries that
Sfold needs.
- Darwin kernel version 9.3.0
	(Other versions may work but have not been tested)
- GCC for Mac OS X available as part of the XCode .dmg package
	(http://developer.apple.com/tools/xcode)
	(Registration required)
- It is recommended that the R .dmg file for Mac OS X provided by
	CRAN be used since this includes Fortran.
	View "R for Mac OS X" at
	(http://cran.r-project.org/bin/macosx)
- If you are not using a version of R that includes the Fortran
	libraries, then G77 for Mac OS X is available at
	(http://hpc.sourceforge.net)
- You must manually set the environment variable
	DYLD_LIBRARY_PATH=path_to_dylib_files
	Use the "find" command to discover where your .dylib files
	are stored on your system.

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Running Sfold
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1. Decompress the downloaded Sfold package:
 gunzip -c sfold-2.2.tar.gz | tar xvf -

2. Change to the extracted directory:
 cd sfold-2.2

3. Configure environment settings:
 ./configure
	A common problem is that R is not found.  One easy solution is
	to make sure that the "R" binary is in your PATH.

4. Inspect ./sfoldenv to make sure the automatically determined 
settings look right to you. If the configure script cannot
locate some of the external programs, e.g. R, you can manually
set the corresponding variable in ./sfoldenv .

5. Test your copy of Sfold by running:
 ./testsfold/testrun
The test compares results generated by your copy of Sfold to 
those from our development machine. If the test fails, check
the indicated log file for more information.

This test takes about 15 seconds on our test system.  If it takes
longer than 3 minutes with no response, it may be that R
cannot be run.  End the test and
check what happens when you try to run "R" at the command line.
You should see R version information followed by a > command
prompt.  Type q() to quit R.

If you get any error messages when trying to run R alone, you
should resolve these first.

6. Execute Sfold:
 ./bin/sfold
Running ./bin/sfold without any argument will give you the
help message on how to run the program. You can run Sfold
from anywhere in your system.


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Output Files
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The Sfold program generates numerous text output files.
sfold.out and sclass.out in your output directory save the 
general messages from standard output/error from which you
can know if your Sfold run was successful. Most of the other
text files contain a header section that defines the formats
and meanings of the data in the output. For a comprehensive
description of the output files, please refer to our online
manual at:
 http://www.wadsworth.org/resnres/bioinfo/sfold/manual.html
and the following papers about features on our Sfold Web 
server:
- Ding, Y., Chan, C.Y. and Lawrence, C.E. (2004) Sfold web 
  server for statistical folding and rational design of 
  nucleic acids. Nucleic Acids Res. 32 Web Server issue, 
  W135-W141.
- Chan, C.Y., Lawrence, C.E. and Ding, Y. (2005) Structure 
  clustering features on the Sfold Web server. 
  Bioinformatics 21, 3926-3928.


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Last updated on August, 2008