Instructions for installation of CLISP, MultiMap source code, CRIMAP
4.1m for use with MultiMap, and RADMAP for RH mapping.


May 1, 1997

	I suggest installing CLISP, MultiMap,CRIMAP and RADMAP all in
separate directories, since they each involve a number of files.

1.  CLISP.  Depending on your level of expertise, installation of
CLISP may not be trival, so I'd be happy to help - just drop me an
e-mail if you would like me to install or help you install CLISP on
your system.

- connect to http://clisp.cons.org/~haible/clisp/binaries/ 

- cd to the directory that most closely matches your machine and
operating system

- retrieve the necessary file - for example, in sun4-sunos4, I needed
clisp.tar.z - follow the installation instructions.  These may vary
slightly from machine to machine.  If the instructions have you
editing the config.lsp file, you can safely ignore them - I never
figured out how to edit this file and it never seemed to matter.

You may be required to edit the Makefile slightly with regard to
pathnames. In the case of sun4-sunos4, I skipped the make-install part
(last step) and set up the following files accordingly instead:

In this example, I have installed CLISP in /usr/local/clisp.  I have
left the important files lisp.run and lispinit.mem in the /base
directory.  You may wish to change this.

I create a file called "clisp", which I would place in /usr/local/bin,
to be my CLISP executable that launches CLISP.  In it I put:

/usr/local/clisp/base/lisp.run -i /usr/local/bin/clisp.init -M 
/usr/local/clisp/base/lispinit.mem

The "-i" flag means that upon launching the application, CLISP will
load in the file "/usr/local/bin/clisp.init".  ***Don't forget to
chmod +x clisp to make it executable.

My standard "clisp.init" file looks like this:

(defun mmap ()
  (load "/home/tara/multimap/src/load-files.lsp") -->this is your path to 
  (load-all-files))				       the MultiMap code
				
(mmap)


	This creates a function called mmap which will cause MultiMap
to be loaded in.  Then, by placing "(mmap)" in the clisp.init file, as
you see above, the mmap function will be executed, so that whenever I
start up CLISP, MultiMap is automatically loaded in.  If you don't
want this to happen, place a semi-colon in front of the call to
(mmap), and it will be commented out.  You can then execute it
yourself after starting up CLISP.

	Sometimes, I want to start a long job and let it run in the
background.  To do this, I put a copy of "clisp" and "clisp.init" in
my working directory.  This "clisp" looks like this:

nohup /usr/local/clisp/base/lisp.run -i ./clisp.init -M
/usr/local/clisp/base/lispinit.mem > run.out & (all on one continuous
line)

and the "clisp.init" might look like this:

(defun mmap ()
  (load "/home/tara/multimap/src/load-files.lsp")
  (load-all-files))

(mmap)
(multimap 13)
(quit)

	Now, when I launch that "clisp" file, CLISP will start, read
in the "clisp.init" file located in the same directory, which will
cause MultiMap to be loaded in and will map chromosome 13, then quit.
All of this will run in the background and screen output will go to
the file "run.out".

- After you have completed the CLISP installation, many files can be
deleted if you want to save space.  Ask me if you are not sure which.

NOTE: in CLISP, if you encounter an error, type abort to return to the
main prompt.  The function (quit) will exit CLISP.



2.  MultiMap

A.  Installing the code.

- get the mmap2.tar file from the ftp site.  This file will contain 23
files of source code, all ending with .lsp.

1.  Make a directory to store the source code.
For example: /usr/local/multimap/src.

2.  Edit the file load-files.lsp as follows:

in the line where the pathname is specified, replace with your path to
the source code:

For example, change

    "/shared/sherlock/usr1/users/tcox/multimap/src/clisp/")))
to
    "/usr/local/multimap/src/")))   	** don't forget the last '/' !!


B.  Compiling the MultiMap code.

- this step need only be done once.  Startup CLISP and load in
MultiMap (it may happen automatically if you follow the instructions
in 1. above).  Then type:

(compile-each-file)

Ignore the many warnings that flash by.  When its completed you can
(quit) CLISP.


3.  CRIMAP

The CRIMAP code has been edited slightly to interface with MultiMap -
the new version is called LISPCRI.  Uncompress and untar crimap.tar.Z.
Simply run the Makefile (type 'make' at UNIX prompt) to compile, and
put the executable 'lispcri' in your path.

4.  RADMAP  (for RH mapping, still beta version)

- get the files radmap4.1.tar and rhdata.tar from src/RHmappping in
the ftp site.  The radmap4.1.tar file will contain several files of
RADMAP source code and a Makefile.  Edit the Makefile so the
appropriate C++ compiler will be used, either C++ for HP C++, or g++
for GNU C++.  Then, simply type make to compile the code.  Put the
radmap executable somewhere in your path, for example, mine is in
/home/tara/bin.  The radmap4.1.tar file also includes two test files,
rad.hyb (data) and rad.ord (marker order).  You should try running
radhyb in the directory where these files are located.  Simply type
"radmap" to execute, it automatically looks for rad.hyb and rad.ord.
The results should look like this:

( ( 9 115 172 18 93 80 99 142 106 123 77 29 90 95 45 23 7 76 145 158 )
0.544 (0.2886 0.1544 0.1102 0.06634 0.06634 0.04394 0.06595 0.08798
0.08827 0.07752 0.07789 0.08943 0.08932 0.06671 0.04446 0.08863 0.0883
0.144 0.1606 ) -391.109)


Two sets of test data are included in rhdata.tar.  In addition, there
is documentation on setting up RADMAP and enough documentation to get
you started with RH mapping in the RHmapping.notes files (use either
the txt version of the Macintosh sea.hqx MSWord5.1 file).  THe
RHtest.doc file describes the test data and how to use it.