Instructions to install this web interface

Requirements:
1) A linux machine (some basic commands like find, and the bash shell are needed).
2) A web server with php.
3) phymls's version modified to analyze coding sequences.
   Hopefully, you can get it at http://www.sanzo.org/ by the 
time you're reading this document.


Install:
1) Put these files wherever your web server has access to.
2) If the computers you want to do the processing, and see the input screen
differ, then edit the "input.html" file's form tag's action attribute as
needed. E.g.
  If you want to actually process things with the phyml in a machine called
 www2, then change to like: 
  http://www2.this.domain.com/~thispath/output.php

Having a server just for the input page, and one for the actual processing/
output page may be beneficial if you've got lots of traffic. But not so much
otherwise.

Optional steps:
1) Get new scripts (for better tuning):
  This interface uses a bunch of scripts to set a better tuning (for better
 performance/accuracy). This version brings already a whole set you can use,
but they may have been updated to for better tuning. These scripts were made
by Professor Sanzo Miyazawa, and you can probably get new ones at the same
page as phyml's version modified to analyze coding sequences:
  http://www.sanzo.org/

  You can also make your own scripts based on the default ones (names must
not be changed).

  You can also have sets of different scripts, and change which set to use 
by modifying the paths.php file, it has some comments on that.

2) Choose or change the settings for the maintenance scripts:
  In order to use this interface without getting your hard disk full, it 
comes with two maintenance scripts.
  a) files_remover.sh:
     Deletes files by quantity. For example, deleting 100 input files (and 
its related data), after 300 files have been processed.
     This script is not used by default.

  b) files_remover_by_date.sh:
     Deletes files by date. For example, deleting all the files that are 2 
weeks older, or so.
     This script is used by default.

  You can either used all, only one, or none of these scripts. You have to
modify the source.php file change that (the run_maintainance_script function
has some comments to help you).
  Obviously, you can make your own scripts in the same fashion.
  In order to modify the amount of files to delete, or the date of the files
to delete, modify these scripts directly (it's commented so you'll be OK).


And that's it! Try it.


If you find any bugs, either send a report, or better, fix it and send it
 back^^.
The original author of this interface wrote it as part of his thesis, so 
can't fix it. But probably Professor Miyazawa will be glad to hear of any
improvement made.
You're also welcomed to do any changes and improvement (either for better 
processing, or just for look and feel) in the spirit of free software and 
expanding knowledge.