/ Bio Informatics

installing TRNAscan-SE

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

Prashanth Madi

Prashanth Madi

I'm a programmer & Tech enthusiast. I work for OpenSource Support Team at Microsoft, but this blog, its content & opinions are my own. I blog about tech, gadgets, code, where we're going & we've been.

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