
Installation of tRNAscan-SE: a tool for finding transfer RNAs
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1) Edit the top of the Makefile. 
   Set the paths and other make variables to suit your system.

   In particular, you need to specify:
   1) where executables are to be installed
   2) where data files are to be installed 
   3) where Perl is already installed on the system
   4) what the Perl binary is called (i.e. 'perl' or 'perl5')
   5) where temporary files will reside 
   6) where to install man pages

2) type 'make' to build the programs

3) type 'make install' to install the programs and man pages.

!! NOTE: If you later manually move the location of 
	 binaries or data files from the directories specified in
	 the 'Makefile', you need to delete the tRNAscan-SE
	 executable, update the locations specified in the Makefile, 
	 and 'make install' again.

4) type 'make testrun' to run tRNAscan-SE on a sample sequence; if the
program runs with no error messages, tRNAscan-SE has been installed
correctly

5) type 'make clean' to clean up.

!! Note: A small Perl script (checkversion.pl) will run in the process of
'make'ing tRNAscan-SE.  If you have specified an invalid location or
version of Perl (<5.0) in the Makefile PERLDIR variable, the make will
fail.  If you plan to install a correct version of Perl AFTER
installing the tRNAscan-SE package, you may short-circut this check by
commenting out the line in the makefile containing 'checkversion.pl'.

tRNAscan-SE is known to build cleanly on a number of different UNIX
platforms and OS's, including:
        SGI, IRIX
        Sun, Solaris
        DEC Alpha, OSF/1
        Intel x86, Linux

Non-ANSI compilers may need one or more -MDEFS defined (see notes in
Makefile if you have a compilation problem).

It is currently maintained under Linux on an Intel PIII-500 using gcc.

