installing TRNAscan-SE

TRNAscan-SE

* tRNAscan-SE is a program for improved detection of transfer RNA genes in genomic sequence.
* URL: http://lowelab.ucsc.edu/tRNAscan-SE/

[edit] Installation

* Get the link location

$ wget http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz
$ cd tRNAscan-SE-1.23/

* Edit Makefile to provide the following details

## where you want things installed
BINDIR = /usr/local/bin
LIBDIR = /usr/local/lib/tRNAscan-SE
MANDIR = /usr/local/man

If you dont change the above path it will install in your home directory $HOME

* Now make the package

$ make
..
..
sqio.c:238: error: conflicting types for ‘getline’
/usr/include/stdio.h:651: note: previous declaration of ‘getline’ was here
make: *** [sqio.o] Error 1
..

* The make did not complete because, there were 2 getline subroutines in 2 different files
* Solution:
o Checked if getline is present in any of the *.c files in this directory
o opened sqio.c and changed all the getline to getLine

$ make

make ran with no error.

NOTE:

* there are some instructions at the end of make. It requires us to run source setup.tRNAscan-SE; rehash for the current session
* Or include a line source /home/krevanna/Desktop/TOOL_TEST/tRNAscan-SE-1.23/setup.tRNAscan-SE in ~/.cshrc
* This wont work because we are in bash shell and it expects us to be in C-shell

* I did not follow the above instructions and i went ahead with make install

$ sudo make install
$ make testrun
$ make clean