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386 DOS installation

IMPORTANT - The programs on this disk will ONLY WORK on a PC with a 386 or better processor. See the Technical Notes section for details of why.


  1. Create a directory on your hard disk. e.g. mkdir ALSCRIPT.

  2. Copy the Contents of the floppy disk into this directory.
        e.g.   copy a:*.* c:\alscript.

  3. Edit your AUTOEXEC.BAT file and add
     C:\ALSCRIPT to your path.

  4. Edit your AUTOEXEC.BAT file and add the following two lines. set DOS4GVM=@ALSCRIPT.VMC set DOS4G=quiet

The first line is an instruction to read instructions from the file ALSCRIPT.VMC. This sets up a permanent swap file on your hard disk. By default, the swap file is about 12MBytes in size. If you do not have this much free space on your disk, then edit the ALSCRIPT.VMC file to reduce the swap file size, or alternatively, do not put this line in your autoexec.bat.

The programs will run without this swap file, but you will be limited in the size of alignment you can process by the amount of RAM you have installed. I have only tested this program on a 486/33 with 8MBytes RAM and a 386/33 with 4MBytes so I do not know the practical limitations of machines with smaller memories. Any feedback would be appreciated.

5. Type AUTOEXEC.BAT to initialise the changes, or better still, reset the computer.

6. You should now be able to run all three programs in the package from anywhere on your disk. msf2blc, clus2blc and alscript. If you get memory allocation errors when you try to run alscript, then use the MAX_NSEQ and MAX_SEQ_LEN commands to reduce the default limits. If the program still won't run, then think about buying some more memory!!

The programs msf2blc and clus2blc should run OK, but if you try to process alignments that are too large for your computer, you may get a "malloc error" which will stop the program. If this happens and you are not using the virtual memory option discussed above, then try adding the line set DOS4GVM=@filename to your autoexec.bat file. If you don't have enough disk space to do this, then buy a bigger disk, or more memory.

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