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