Getting Started

The following instructions for installing the tRNAscan-SE package also appear in the ``INSTALL'' text file:

1. Edit the top of the Makefile. Set the paths and other make variables to suit your system.

   In particular, you need to specify:

   • where executables are to be installed
   • where data files are to be installed
   • where Perl is already installed on the system
   • what the Perl executable is called (i.e. ``perl'' or ``perl5'')
   • where temporary files will reside
   • 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.

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), and Intel x86 (Linux).

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'.

Once installed, the user may wish to work through several of the examples included (Section 6 of this document) to get a quick feel for the program's operation and some of the most commonly used command line options. A description of the default run mode and output appears in Section 4, and a description of each of the program options is included in Section 5 of this document.