INSTALL.ME

MAPMAKER 3.0 and MAPMAKER/QTL 1.1 INSTALLATION GUIDE
(c) Copyright 1992 Whitehead Institute for Biomedical Research

Here,we describe how you should copy the MAPMAKER files on to your computer and 
how to then complete the installation process. In the preceding "General 
Information" section (and in the READ.ME file), we describe the types of 
systems which can run MAPMAKER. It is important that you read this section 
first to make sure your computer is appropriate, before proceeding with the 
instructions below.  Separate sections below describe MAPMAKER installation on 
(1) PC's, (2) Sun SPARCstations, (3) A/UX Macintoshes, and (4) other computers.


(1) INSTALLING ON A PC COMPATIBLE RUNNING DOS

From a DOS prompt, make a new directory named MAPMAKER on your hard
disk.  If you have received MAPMAKER on floppy disk, simply "CD" into this 
directory and copy the files on the MAPMAKER floppy disk(s) into it.  The 
commands to do this will be something like:

    MKDIR C:\MAPMAKER
    CD C:\MAPMAKER
    COPY A:*.* C:

If instead you retrieved MAPMAKER from the Internet via FTP, you should move 
the files you retrieved into this MAPMAKER directory now, as above.

You should now have READ.ME and INSTALL.ME files (this document, actually) as 
well as two compressed PKZIP self-extracting archives named MAPM3PC1.EXE and 
MAPM3PC2.EXE. To extract the other MAPMAKER files from this archive, you should 
simply type:

    MAPM3PC1 /D
    MAPM3PC2 /D

Many more files will now be in this directory, including:

MAPMAKER.BAT  - The actual executable for MAPMAKER/EXP 3.0
MAPMAKER.PIF  - MAPMAKER launcher for Windows 3.1
MAPMBIN.EXE   - The binary program for MAPMAKER 3.0 (*)
MAPMAKER.HLP  - The on-line help information for MAPMAKER 3.0 
QTL.BAT       - The actual executable for MAPMAKER/QTL Version 1.1
QTL.PIF       - MAPMAKER/QTL launcher for Windows 3.1
QTLBIN.EXE    - The binary program for MAPMAKER/QTL Version 1.1 (*)
QTL.HLP       - The on-line help information for MAPMAKER/QTL 1.1
SAMPLE.RAW    - A sample data set, used in the tutorials
SAMPLE.IN     - Sample batch file (commands from the MAPMAKER/EXP tutorial)
SAMPLE.INP    - Sample batch file (commands to set up the QTL tutorial)
SAMPLE.INQ    - Sample batch file (commands from the MAPMAKER/QTL tutorial)
MOUSE.RAW     - Large sample data set for MAPMAKER/EXP tutorial
MOUSE.PRE     - Initialization file for MOUSE.RAW
MOUSE.IN      - Sample batch file (commands from the MAPMAKER/EXP tutorial)
DOS4GW.EXE    - The run-time package used by the programs (from WATCOM *)
MAPM.VMC      - The virtual memory set up file used by DOS4GW.EXE
READ.ME       - The Release Notes, including license information
INSTALL.ME    - This Installation Guide
FEED.ME       - Instructions for preparing data files
CHANGE.ME     - Change list, bug list and to-do list
COVER.ME      - Cover letter
GSCRIPT <DIR> - Portions of the FSF's GhostScript package

If this succeeds, you can now delete the archives:


    DEL MAPM3PC1.EXE
    DEL MAPM3PC2.EXE

To run MAPMAKER, your PC must have EXTENDED memory active (for most data sets 8 
megabytes or more is best, 4 may or may not suffice). The DOS command MEM will 
tell you how much extended memory is available. If this number is zero, but 
your PC has extended memory installed, check your CONFIG.SYS file for a line 
like:

    DEVICE=C:\DOS\HIMEM.SYS
 or DEVICE=C:\WINDOWS\HIMEM.SYS

(You can use the DOS editor or Windows Notepad to do this.) If this line is not 
present, you need to add it (although you should consult the DOS and/or Windows 
documentation first). Remember that EXTENDED memory is entirely different from 
EXPANDED or LIM/EMS (as is provided by EMM386).

In addition, the lines:

    DEVICE=C:\DOS\ANSI.SYS
    BREAK=ON

should also be in your CONFIG.SYS file.

You will also likely find it convenient to have the MAPMAKER directory listed 
in your PATH, which is usually set-up in your AUTOEXEC.BAT file. This way, you 
can simply type "MAPMAKER" or "QTL" at a DOS prompt to run MAPMAKER or 
MAPMAKER/QTL respectively. To use the on-line help feature, you also need to 
separately indicate which directory the help files are in (as well as other 
files the MAPMAKER programs use). These concerns both also hold true for the 
GhostScript package, if you wish to use it. The appropriate commands in your 
"AUTOEXEC.BAT" file should read something like:

    PATH C:\DOS;C:\WINDOWS;C:\MAPMAKER;C:\MAPMAKER\GSCRIPT;
    SET MAPM_LIB=C:\MAPMAKER
    SET GS_LIB=C:\MAPMAKER\GSCRIPT

After making these changes, you will then need to completely restart your 
computer (e.g. Hit Control-Alt-Delete). Consult your DOS documentation or your 
PC support person if you have any questions.

With the programs installed this way, to run MAPMAKER or MAPMAKER/QTL 
(respectively) you can simply type at a DOS prompt:

    MAPMAKER
or  QTL

It should not matter what directory you are presently in. In particular, you 
will find it most convenient to make a separate directory (or directories) for 
all of your personal data files and output, and to "CD" into that directory 
before you run MAPMAKER.

The MAPM.VMC file included describes to your computer the memory requirements 
for running MAPMAKER and MAPMAKER/QTL. If you use particularly large data sets, 
you may need to change the "virtualsize" limit set in this file. You can also 
edit this file with a standard text editor.

The above comments assume, of course, that you have DOS 5.0 installed in the 
C:\DOS directory and Windows 3.1 (if you have it) in the C:\WINDOWS directory. 
If not, modify the above instructions accordingly.  If you are installing 
MAPMAKER on something other than your drive C: in directory \MAPMAKER, you will 
also need to edit the contents of the MAPMAKER.BAT, QTL.BAT, and MAPM.VMC files 
accordingly.

Lastly, you may find it convenient to run MAPMAKER and MAPMAKER/QTL with more 
lines of text on the screen at once (a feature allowed by EGA and VGA 
displays). To do this, you can simply alter the "MODE" and "SET" commands in 
the included "MAPMAKER.BAT" and "QTL.BAT" files by first removing the "REM" 
words and then changing the command to specify "lines=43" or "lines=50" (as 
opposed to "lines=25"). These modes work particularly well within Windows, more 
particularly if you change the font of the DOS window.

* You should not try to run these executables directly.  Use the 
  ".BAT" scripts or ".PIF" files instead.

RUNNING MAPMAKER WITH WINDOWS 3.1

MAPMAKER and MAPMAKER/QTL will run correctly in a "DOS Prompt" window under 
Microsoft Windows 3.1 running in "386-Enhanced" mode using the above 
installation method.  The programs will run in the background, allowing them to 
perform lengthy computations while you use the computer for other things 
(performance however, may not be the best).

For MAPMAKER and MAPMAKER/QTL to work, Windows must make a sufficient amount of 
"Virtual Memory" available to these programs, which it may not be doing by 
default. To make virtual memory available, select the Control Panel icon in the 
Windows Program Manager.  Then, select the "386 Enhanced" icon, and click on 
the "Virtual Memory" button in the dialog box that appears. Increase the size 
to 20,000 KB or more (if possible) and then exit and restart Windows (you can 
use either a temporary or permanent swap file). Note that the precise amount 
you need depends on the size of your data sets and the number of other programs 
you want to run at the same time.

For your convenience, "PIF" files are included for both MAPMAKER and 
MAPMAKER/QTL. If you simply drag these from a "File Manager" window into the 
"Program Manager", you can simply start the MAPMAKER programs by double 
clicking on the appropriate icon. However, you may then need to use MAPMAKER's 
"CD" command to go into the appropriate directory containing your data files.

DISPLAYING AND PRINTING POSTSCRIPT GRAPHICS

The MAPMAKER and MAPMAKER/QTL "draw" commands produce standard level 1 
PostScript files (text files with the extension ".PS") which can be displayed 
and printed in a number of ways. They print "as-is" simply by sending them to a 
PostScript printer using the DOS "PRINT" command, although we have tested this 
using an Apple LaserWriter.  Be aware that many LaserJet compatible printers do 
NOT by default support PostScript.

You can also display these graphics under Windows 3.1 using the "GhostScript" 
package included with MAPMAKER. In the Windows "File Manager" you should 
"associate" the application:

    C:\MAPMAKER\GSCRIPT\GSWIN.EXE

with files ending in the extension ".PS" (consult your Windows documentation 
for details). This way, when you double-click on a ".PS" file, including those 
generated by MAPMAKER, the graphics will be displayed in a scrolling window 
using GhostScript. Two windows in fact are opened: a GhostScript transcript 
window, and the graphic image itself. Multi-page graphics will be displayed one 
page at a time: simply hit the return key in the transcript window to view 
successive pages. When viewing is complete, type "quit" (in lower case letters) 
in the transcript window to exit GhostScript. As of this version, GhostScript 
can have only one file open at a time, and it does not seem to understand drag-
and-drop or cut-and-paste actions.

GhostScript can also output directly to a EGA or VGA monitor, without Windows, 
although the type is so small that this feature is only useful as a "Print 
Preview" function.

GhostScript can allegedly also be used to print PostScript graphics on a non-
PostScript Hewlett-Packard LaserJet or DeskJet or Epson 9-pin or 24-pin 
compatible printer. You can do this by typing the "GS386" command to DOS with 
the appropriate arguments as described in the GhostScript documentation. If 
GhostScript is not satisfactory, various other third-party packages can also be 
used to display or print the PostScript files. It is also possible to move the 
PostScript files to another computer (PC or otherwise) with a PostScript 
printer attached for printing (PostScript files contain only simple ASCII 
text). 

Exactly how you get the PostScript files displayed or printed is a technical 
problem addressed by many commercial and free products, and it depends greatly 
on your exact system configuration. Consult your computer support people for 
details. Because system configurations vary so greatly, we cannot provide any 
help in these matters.

GhostScript documentation is included in the text files "README" and "USE.DOC" 
in the "GSCRIPT" directory.

KNOWN INCOMPATIBILITIES

The virtual memory required by MAPMAKER is incompatible with disk compression 
utilities such as STACKER. If a similar utility is active on your PC, you may 
need to remove it before MAPMAKER will run properly. This may require 
reformatting your hard disk - ask your PC support people.

MAPMAKER seems to have problems when launched from the visual DOS shell 
(DOSSHELL). We do not recommend using MAPMAKER with DOSSHELL - exit to DOS 
before running MAPMAKER. MAPMAKER is definitely incompatible with DOSSHELL's 
"task switching" feature - use Windows instead.

When running under Windows, MAPMAKER often exits completely (WITHOUT updating 
your data files) when you hit Control-C or Control-Break, rather than having 
this simply stop the command MAPMAKER is currently performing. This sometimes 
(although rarely) happens under ordinary DOS also, and there is little we can 
do about it (it's a system bug). Save your files often and use Control-
C/Control-Break sparingly, if at all.

We have one 4+ year old 386 PC clone with a very old AMI BIOS which will not 
run MAPMAKER correctly. We don't know why.

Some old 386 clones used a 287 (not a 387) as their math coprocessor -these 
systems may not work.

As we have not had the opportunity to test the programs on the wide 
variety of PC systems and setups available, there are likely MANY other 
incompatibilities with particular device drivers, memory managers, anti-virus 
utilities, "TSR" programs, networks, shells, etc. If you discover any other 
incompatibilities, please tell us, so that we can note them here.


(2) INSTALLING ON A SPARCSTATION RUNNING SUNOS

You have two choices when installing MAPMAKER: (1) You can simply install 
MAPMAKER into your personal account (or into a shared account, which multiple 
users log into), or (2) you can install MAPMAKER as a system wide resource 
available to all users (e.g. in /usr/local or some such place).

We detail the former type of installation here -- an individual with some level 
of Unix expertise and the system manager (root) password will be easily able to 
accomplish the later using these instructions here as a guideline.

From a Unix prompt (e.g. in a Command Tool window), make a new directory named 
"mapmaker" in your account's home directory (be sure to use lower case). If you 
received MAPMAKER on floppy disk, simply "cd" into this directory and copy the 
files on the MAPMAKER floppy disk into this directory. The commands to do this 
will be something like:

    mkdir ~/mapmaker
    cd ~/mapmaker
    bar xvpf /dev/rfd0c
    eject

If instead you retrieved MAPMAKER from the Internet via FTP, you should move 
the files you retrieved into the "mapmaker" directory now, using the "mv" 
command.

You should now have READ.ME and INSTALL.ME files (this document, actually) and 
a compressed tar archive named "mapm3-sparc.tar.Z". To extract the actual 
MAPMAKER files from this archive, you should type:

    uncompress mapm3-sparc.tar.Z
    tar xvpf mapm3-sparc.tar

Many more files will now be in this directory, including:

mapmaker      - The executable program for MAPMAKER 3.0
mapmaker.help - The on-line help information for MAPMAKER 3.0
xmapmaker     - A script for running MAPMAKER under OpenWindows or X11
qtl           - The executable version of MAPMAKER/QTL Version 1.1
qtl.help      - The on-line help information for MAPMAKER/QTL 1.1
xqtl          - A script for running MAPMAKER/QTL under OpenWindows or X11
sample.raw    - A sample data set, used in the tutorials
sample.in     - Sample batch file (commands from the MAPMAKER/EXP tutorial)
sample.inp    - Sample batch file (commands to set up the QTL tutorial)
sample.inq    - Sample batch file (commands from the MAPMAKER/QTL tutorial)
mouse.raw     - Large sample data set for MAPMAKER/EXP tutorial
mouse.prep    - Initialization file for MOUSE.RAW
mouse.in      - Sample batch file (commands from the MAPMAKER/EXP tutorial)
READ.ME       - The Release Notes, including License information
INSTALL.ME    - This Installation Guide
FEED.ME       - Instructions for preparing data files
CHANGE.ME     - Change list, bug list and to-do list
COVER.ME      - Cover letter
ghostscript/  - The GhostScript package from the Free Software Foundation

If this succeeds, you can now delete the archive:

    rm mapm3-sparc.tar

You will also likely find it convenient to have the "mapmaker" directory
listed in your "path", which is usually set-up in the ".cshrc" or ".login" file 
in your home directory. This way, you can simply type "mapmaker" or "qtl" at a 
Unix prompt to run MAPMAKER or MAPMAKER/QTL respectively. To use the on-line 
help feature, you also need to separately indicate which directory the help 
files are in (as well as other files the MAPMAKER programs use). These concerns 
both also hold true for the GhostScript package, if you wish to use it. The 
appropriate commands in your ".cshrc" file might read something like:

set path=(. /bin /usr/bin /usr/ucb /usr/local/bin /usr/openwin/bin\
/usr/openwin/bin/xview /home/joe/mapmaker /home/joe/mapmaker/ghostscript)
rehash
setenv MAPM_LIB /home/joe/mapmaker
setenv GS_LIB /home/joe/mapmaker/ghostscript

Note that the backslash at the end of the first line above indicates that the 
command spans two lines, and that the backslash MUST be the very last character 
on the line. Instead, you could make this one long line.

After making these changes, you may need to completely log out and log back in 
again. The above instructions above assume that you are a "C-Shell" user (the 
default on Suns), and need to be changed for those who use sh, ksh, bash, or 
some other Unix shell. Consult your Sun documentation or your Unix support 
person if you have any questions.

With the programs installed this way, to run MAPMAKER or MAPMAKER/QTL 
(respectively) you can simply type at a Unix prompt:

    mapmaker
or  qtl

It should not matter what directory you are presently in. In particular, you 
will find it most convenient to make a separate directory (or directories) for 
all of your personal data files and output, and to "cd" into that directory 
before you run MAPMAKER.

RUNNING MAPMAKER WITH SUNVIEW, OPENWINDOWS, OR X-WINDOWS

As we mentioned earlier, MAPMAKER runs correctly under SunView, OpenWindows, 
and X-Windows using a standard terminal-emulator program, such as Command Tool 
(cmdtool), Shell Tool (shelltool), or xterm. However, Sun's Command Tool 
program, in both SunView and OpenWindows (in both versions 2.0 and 3.0), has a 
nasty design flaw (in our humble opinion) which causes MAPMAKER's command line 
editing to fail. Sun is aware of this problem and claimed years ago that they 
would fix it someday.

Possible solutions to this problem are:

(1) Do not use MAPMAKER command line editing features. In Command Tool, you can 
use the limited command editing capabilities it provides.

(2) Run MAPMAKER in a "Shell Tool" window instead. Unfortunately, Shell Tool 
does not provide a scrollbar to review MAPMAKER output which has scrolled off 
the screen. The "review output" command provides one slightly less convenient 
way to do this, however.

(3) Under OpenWindows, run MAPMAKER in a "xterm" window instead. This way you 
get both a scrollbar and command line editing.  Xterm's scrollbar is a tad 
peculiar however -- play with all of the mouse buttons and you'll figure it 
out. Cut-and-paste between xterm and OpenLook programs is also peculiar, 
although we rarely find this a problem. Contact Sun for details.

(4) Use "real" X-Windows instead of OpenWindows (or SunView).

In OpenWindows 2.0, Sun provided xterm in /usr/openwin/demo for some 
strange reason, thus if you simply type "xterm", SunOS will usually not find 
the command. In OpenWindows 3.0, it is correctly in /usr/openwin/bin. Note that 
the version 2.0 xterm produces warnings you may safely ignore.

The "xmapmaker" and "xqtl" scripts we have provided start an xterm window with 
MAPMAKER or MAPMAKER/QTL inside, respectively.  You should be able to type into 
your CONSOLE window or into a Command Tool:

	xmapmaker &
or	xqtl &

in which case a new window will open running MAPMAKER or MAPMAKER/QTL. The "&" 
symbol of course indicates that the program should be run "in the background", 
as is usually appropriate for programs which open their own windows. Consult 
your Sun documentation for details.

Using "olwm", the OpenWindows "file manager", or "binder", it is possible to 
provide menu entries and/or icons which more simply start MAPMAKER and 
MAPMAKER/QTL. Consult your Sun documentation for details. We do not use 
OpenWindows, so we can not offer any help on this.

DISPLAYING AND PRINTING POSTSCRIPT GRAPHICS

The MAPMAKER and MAPMAKER/QTL "draw" commands produce standard level 1 
PostScript files (text files with the extension ".ps") which can be displayed 
and printed in a number of ways. They print "as-is" simply by sending them to a 
PostScript printer using the Unix "lpr" command, although we have only tested 
this using an Apple LaserWriter.

You can also display these graphics under OpenWindows or X-Windows 
using the "GhostScript" package included with MAPMAKER. In a window with a Unix 
prompt (e.g. Command Tool, xterm, etc.) simply type something like:

	gs mygenome.ps

and a window will open displaying the named PostScript file. Multi-page 
graphics will be displayed one page at a time: simply hit the return key in the 
transcript window to view successive pages. When viewing is complete, type 
"quit" (in lower case letters) in the Unix window to exit GhostScript. As of 
this version, GhostScript can have only one file open at a time, and it does 
not understand OpenWindows/X-Windows actions such as cut-and-paste or drag-and-
drop. More sophisticated PostScript previewers are available -- for example, if 
you have Internet access, look for "ghostview" or "gpsview" on prep.ai.mit.edu.

As of OpenWindows version 2.0, Sun's "pageview" command has many bugs which 
prevent it from correctly displaying MAPMAKER's PostScript graphics output. We 
do not know how well the 3.0 pageview works, although we recommend that you use 
the GhostScript package instead. GhostScript has the added advantage of working 
on PC's, Mac's, X-Terminals, or other types of workstations connected to your 
Sun using X-Windows.

GhostScript claims it can also be used to print PostScript graphics on a non-
PostScript Hewlett-Packard LaserJet or DeskJet or Epson 9-pin or 24-pin 
compatible printer. We have not tried this. If GhostScript is not satisfactory, 
various third-party packages can also be used to display or print the 
PostScript files, including the Sun NewsPrint product. We have
NOT tried NewsPrint or GhostScript with any type of printer. It is also 
possible to move the PostScript files to another computer (Sun, Mac, or PC) 
with a PostScript printer attached for printing (PostScript files contain only 
simple ASCII text).

Exactly how you get the PostScript files displayed or printed is a technical 
problem addressed by many commercial and free products, and it depends greatly 
on your exact system configuration. Consult your computer support people for 
details. Because system configurations vary so greatly, we cannot provide any 
help in these matters.

GhostScript documentation is included in the text files "README" and "use.doc" 
in the "ghostscript" directory.


(3) INSTALLING ON A MACINTOSH RUNNING A/UX

Exactly how you install MAPMAKER under A/UX depends exactly on how A/UX is 
configured on your system. Because we suspect that many A/UX users will be 
installing A/UX only to use MAPMAKER, we first provide a few hints about that 
process:

(1) We have installed UNIX systems on many hardware platforms, and have found 
the A/UX documentation to be the best we have encountered. Moreover, the 
integration between A/UX and System 7 is excellent, and most proficient Mac 
users will have no problem installing A/UX. Installing networking under A/UX is 
slightly different (however straightforward) from doing it under ordinary 
System 7, and you may want to have your computer support person take a look at 
the A/UX manual. 

(2) The Apple documentation correctly states that a complete installation of 
A/UX requires 160Mb of disk space. However, a minimal A/UX 3.0, more than 
adequate for running MAPMAKER, requires only about 60Mb. The only package you 
need to install for MAPMAKER is the "Core A/UX System", although the 
"Networking Capability" and "UNIX Printing" packages will be needed to use an 
Apple LaserWriter. The "Commando Dialogs" may be useful if you intend to make 
much use of the A/UX command line interface, but are optional. No others are 
usually required.

(3) A very simple A/UX installation configuration is adequate, particularly if 
you are no more worried about security than your average Mac user. We have 
users simply log into the "Guest" account, which we leave without a password. 
The machine is left running this way most of the time. We did give the "root" 
account a password and we log into it only when we need to perform a system 
set-up function, and we log out immediately afterwards (this helps prevent 
other users from inadvertently messing up the system). Note that if you enable 
TCP/IP networking and you are on a network, then it is possible to log into 
your A/UX machine from anyplace on the net, in which case stricter uses of 
passwords is a good idea.

(4) Really do read the A/UX README file, provided on floppy disk. In 
particular, we were confused by the problem it mentions about disks greater 
than 160Mb having an un-mounted partition (page 2). The instructions it gives 
leave out a step, needed if you wish ordinary users to have access to this 
folder. After the "mkdir" command, type:

    chmod rwx /users2

It's also handy to make an alias of the "/users2" folder in the Finder and drag 
it onto the Mac desktop.

(5) If you have multiple hard disks, you only need to have A/UX format the disk 
it is installed on -- other disks can be left in any System 7 compatible format 
(although you should note the A/UX README file's comments about old disk 
drivers -- LaCie's SilverLining has worked well for us with A/UX). However, 
note that MAPMAKER input and output can ONLY be stored in a folder on an A/UX 
partition or disk, which can also store Mac files as usual.

(6) A good source of compatibility and technical information about A/UX is the 
comp.unix.aux bulletin-board on the Internet. The Frequently Asked Questions 
(FAQ) document they publish is very helpful, although rather technical. A copy 
as of December of 1992 is included as the file AUX.FAQ.

(7) Remember that A/UX comes with one year of toll-free technical support by 
phone. Use this! In particular, they can help with the few exiting 
compatibility problems between A/UX and System 7 programs (however, almost all 
applications and many INITs are compatible).

(8) It is a good idea to make a separate System Folder for each user. This way, 
in case you/they add an extension which doesn't work right or otherwise screws 
the system up, you can log in as "root" and fix it (otherwise, nobody can log 
in). To make your own Sstem Folder, when logged in as Guest (or as the user in 
question) type into a CommandShell window:

    systemfolder

You only need to do this once. Be sure the capitalization and (lack of) spacing 
is correct.

(9) You may find the A/UX TextEditor program for editing, reading, and printing 
the many text files used for input and output by MAPMAKER.  It's a good idea to 
make an alias of this program in your Apple Menu Iems folder (it's in the "bin" 
folder in the "mac" folder on the "/" drive).  Any file capable of producing 
ASCII text files will work, although formated files (e.g. from a word processor 
or spreadsheet) will not be readable by MAPMAKER.

(10) A/UX is not fast. We find performance good on a Quadra 700, and acceptable 
on a IIci (with a cache card). We do not recommend slower Macs.


INSTALLING MAPMAKER AND MAPMAKER/QTL

You have two choices when installing MAPMAKER: (1) You can simply install 
MAPMAKER into your personal account (or into a shared account, which multiple 
users log into, such as the "Guest" account), or (2) you can install MAPMAKER 
as a system wide resource available to all users (e.g. in /usr/local or some 
such place).

We detail the former type of installation here -- an individual with some level 
of A/UX expertise and the system manager (root) password will be easily able to 
accomplish the later using these instructions here as a guideline.

Log into A/UX. Using the Finder, make a new folder inside your "home directory 
folder" named "Mapmaker" (note the capitalization, and make this name exact). 
If you received MAPMAKER on floppy disks, open this new folder and drag the 
contents of the MAPMAKER floppy disks here. 

If instead you received MAPMAKER via FTP, you can drop the files you retrieved 
from the network here. The main file, "mapm3-aux.hqx" is a BinHex file.  
Depending on how you retrieved it, you may need to apply BinHex 4.0 (or a 
compatible program) to convert it into Macintosh format. Ask your support 
people for details.

You should now have READ.ME and INSTALL.ME files (this document, actually) and 
a self-extracting Compact-Pro archive named "Mapmaker3.archive". To extract the 
actual MAPMAKER files from this archive, simply double click on the archive and 
make sure that your new Mapmaker folder is indicated in the dialog box which 
then pops up.

Many more files will now be in this folder, including:

mapmaker      - The executable program for MAPMAKER 3.0
mapmaker.help - The on-line help information for MAPMAKER 3.0
qtl           - The executable version of MAPMAKER/QTL Version 1.1
qtl.help      - The on-line help information for MAPMAKER/QTL 1.1
sample.raw    - A sample data set, used in the tutorials
sample.in     - Sample batch file (commands from the MAPMAKER/EXP tutorial)
sample.inp    - Sample batch file (commands to set up the QTL tutorial)
sample.inq    - Sample batch file (commands from the MAPMAKER/QTL tutorial)
mouse.raw     - Large sample data set for MAPMAKER/EXP tutorial
mouse.prep    - Initialization file for MOUSE.RAW
mouse.in      - Sample batch file (commands from the MAPMAKER/EXP tutorial)
.cshrc        - A set-up file for the A/UX CommandShell
READ.ME       - The Release Notes, including license information
INSTALL.ME    - This Installation Guide
FEED.ME       - Instructions for preparing data files
COVER.ME      - Cover letter
CHANGE.ME     - Change list, bug list and to-do list

If this succeeds, you may now trash the "Mapmaker3.archive" file.

MAPMAKER requires that your "Command Shells" be set up in such a way that they 
indicate to MAPMAKER where to find certain files it needs, and other 
"preferences"-type information.  Again, because most A/UX users will only use 
"Command Shell" windows to run MAPMAKER, we have provided a simple ".cshrc" 
file which contains the appropriate settings. You should move this file into 
your "home directory folder" now, replacing the existing one (note that in the 
finder, this file is diaplayed with a leading bullet character rather than a 
period -- this is correct, don't change it). If you in fact already have a 
customized ".cshrc" file (other than the default one A/UX gave you), you will 
need to merge their contents together using the A/UX Text Editor, and the 
instructions provided for setting your "path" and other "environment variables" 
above for SPARCstations may be relevant.

After making these changes, you may need to completely log out and log back in 
again. The above instructions above assume that you are a "C-Shell" user (the 
default for A/UX), and need to be changed for those who use sh, ksh, bash, or 
some other Unix shell. Consult your A/UX documentation or a Unix support person 
for questions.

With the programs installed this way, to run MAPMAKER or MAPMAKER/QTL 
(respectively) you can simply type at a prompt in a CommandShell window:

    mapmaker
or  qtl

It should not matter what folder (directory) you are presently in. In 
particular, you will find it most convenient to make a separate folder (or 
folders) for all of your personal data files and output, and to "cd" into that 
folder in the Command Shell before you run MAPMAKER, as described in the A/UX 
documentation.  Recall that the A/UX Command Shell is sensitive to upper and 
lower case letters, and it is easily confused by file names containing spaces.

Alternatively, you can start MAPMAKER or QTL by simply double-clicking on the 
respective file in the finder, and then hitting the default button in the 
"Commando" dialog which appears. In this case however, you mey need to then use 
the MAPMAKER or MAPMAKER/QTL "cd" command to go into the folder containing your 
data files before you begin work.

Unix and the Mac Finder have different file naming conventions which can create 
confusion.  In particular, Unix is case sensitive, doesn't generally like 
spaces in file names, and people usually place "extensions" (for ex: ".raw") at 
the end of file names to tell what type of file it is.  We suggest that you use 
the Unix naming conventions for both folders and files you will use with 
MAPMAKER.

DISPLAYING AND PRINTING POSTSCRIPT GRAPHICS

The MAPMAKER and MAPMAKER/QTL "draw" commands produce standard level 1 
PostScript files (text files with the extension ".ps") which can be displayed 
and printed in a number of ways. They print "as-is" simply by sending them to a 
PostScript printer (such as an ordinary Apple LaserWriter on LocalTalk) using 
the A/UX "lpr" command, as described in the A/UX documentation (see the 
Networking book, under "Printing"). For example, you can use MAPMAKER's 
"system" command to bring up an A/UX prompt, and type something like:

    lpr mygenome.ps

Alternatively, a Mac program such as SendPS or others (available in some public 
domain collections) will do the same thing. Printing these files using the A/UX 
Text Editor will not have the desired effect, however. Also, it is not possible 
to print these files on any QuickDraw printers (laser or dot-matrix) without a 
PostScript emulator like "GhostScript" or "Freedom of Press".

You can also display these graphics under the X-window system (including MacX) 
using a PostScript previewer such as the freely available "GhostScript" 
package. We do not suspect that most MAPMAKER A/UX users will use X-Windows 
however, and so we have not included this package. Rumor has it that a native 
Macintosh version of GhostScript may exist, although we have not tried it. 

Exactly how you get the PostScript files displayed or printed is a technical 
problem addressed by many commercial and free products, and it depends greatly 
on your exact system configuration. Consult your computer support people for 
details. Because system configurations vary so greatly, we cannot provide any 
help in these matters.


(4) INSTALLING ON ANOTHER TYPE OF COMPUTER

We distribute MAPMAKER for DOS, Sun, and A/UX systems because we belive those 
systems represent the greatest installed base of users (and these computers 
have floppy disk drives, makeing it easy to send executables). However, we know 
that the MAPMAKER programs will easily compile and run correctly on:

    DECStation (MIPS-based) systems running Ultrix 4.x.

In addition, we have heard that previous versions of MAPMAKER had been made to 
work correctly on:

    IBM RS/6000 Unix Systems
    Silicon Graphics Systems
    HP Series 700 Unix Systems
    DEC VAX/VMS systems, both with and without DEC's POSIX package
    Various 386 and 486 versions of Unix

Other platforms we would like to see work would include:

    DEC Alpha systems running OSF/1 and/or OpenVMS
    Windows NT on anything (Intel, MIPS, Alpha)

As we have no experience ourselves with these platforms and the new version of 
MAPMAKER, we must wait until some user tries them and reports back to us about 
what is required to make MAPMAKER work (if it really works at all).

WHAT YOU WILL NEED

A computer. Lots of memory. A C compiler (K&R, not ANSI). A good deal of disk 
space. Somebody who has basic experience with C programming on this platform 
and who has anywhere from 15 minutes to a few days free.

The MAPMAKER source code is available on the Internet by Anonymous FTP from 
genome.wi.edu. Get the README file there for details. The code is provided as a 
compressed tar archive which can be extracted using Unix commands like:

	uncompress mapm3-source.tar.Z 
	tar xvf mapm-source.tar

Versions of the GNU readline and GhostScript packages are included which we 
know work with MAPMAKER.  Check the documentation included with them for 
installation instructions and license agreement.

If you have no Internet access, we may be able to send you source code on tape, 
although if so, we may charge you a distribution fee for it, and we can 
generate only limited types of tapes. Contact:

	Mark Daly
	Whitehead Institute for Biomedical Research
	9 Cambridge Center
	Cambridge, Massachusetts  02142  USA
	FAX 617-258-6505
	Internet Email: mjdaly@athena.mit.edu

As with MAPMAKER itself, the source code is redistributable under the MAPMAKER 
license terms. You can copy it from your colleagues or collaborators (or 
competitors), under the license's terms.

WHAT YOU SHOULD DO

You will need to slightly edit the source files. Look in "Makefile", 
"lib/syscode.c" and "lib/system.h". A C programmer will likely know what to do, 
given the comments in those files. A makefile is provided, so the programs 
should compile itself if you type the command "make".  The hassles will be 
greatest on operating systems which are most dissimilar to Berkely (BSD) Unix.

If you succeed in making MAPMAKER work on another type of computer, please tell 
us. If you fail, please tell us -- we may (or may not) be able to offer help.  
We'd like to at least know, so we can tell others.

While it is possible to compile MAPMAKER on a Macintosh (using either MPW C or 
ThinkC 5.0 w/32-bit integers), we have not been able to make these versions 
reliable -- they crash often, likely because of the primitive and non-standard 
nature of the Macintosh's memory manager. The Macintosh port of MAPMAKER 
remains available from DuPont, as described above.

MODIFYING MAPMAKER

You are welcome to modify MAPMAKER for your own uses. In addition, you can 
distribute modified versions, under the terms of our license agreement.

To add commands, you need only to write the command function in C (use our 
functions as a guideline), and add an entry to the command table in main.c. 

To interface MAPMAKER to a database, see the comments in database.c Contact 
Mark Daly, at the address above, if you have any questions.


Ver 3b: S. Lincoln 12/92