sff_extract (presumably from here) is a Python script. Assuming a) you have Python installed and b) the first line of the file points to #!/usr/bin/env python (or the location of your Python interpreter) then a simple

chmod 755 sff_extract; ./sff_extract

(or copy to a bin directory in your $PATH) should be sufficient. If you want to call it explicitly then

python sff_extract

will also work.

After following the instructions you gave me and installed python. the command went as follows

[admin@ty10063-per ~]$ cd Desktop
[admin@ty10063-per Desktop]$ ls
chevreux_thesis_MIRA.pdf
flower
HKI_B_TCMID15_080410.fasta
HKI_B_TCMID15_080410.qual
mira_3.2.0_prod_linux-gnu_i686_32_static
mira_3.2.0_prod_linux-gnu_i686_32_static.tar.bz2
Python-2.6.5
sff_extract
TEST ERROR MIRA3
[admin@ty10063-per Desktop]$ cd mira_3.2.0_prod_linux-gnu_i686_32_static
[admin@ty10063-per mira_3.2.0_prod_linux-gnu_i686_32_static]$ ls
bin              docs           minidemo       scripts      THANKS
CHANGES_old.txt  docs_3rdparty  mira_assembly  stickleback
CHANGES.txt      LICENCE        README         support
[admin@ty10063-per mira_3.2.0_prod_linux-gnu_i686_32_static]$ sudo cp bin/<em> /usr/local/bin
[sudo] password for admin: 
[admin@ty10063-per mira_3.2.0_prod_linux-gnu_i686_32_static]$ sudo cp scripts/</em> /usr/local/bin
[admin@ty10063-per mira_3.2.0_prod_linux-gnu_i686_32_static]$ chmod 755 sff_extract;./sff_extract
chmod: cannot access `sff_extract': No such file or directory
bash: ./sff_extract: No such file or directory
[admin@ty10063-per mira_3.2.0_prod_linux-gnu_i686_32_static]$

QUESTION:

Why do i get the error message No such file or Directory

Thanks alot Daniel