Mac Osx 10.8 and Samtools problems

[neophte]

Hi

I am a newbie to bioinformatics!

I having problems running samtools from my terminal using mac osx v10.8 on my pro. I've downloaded and unpacked v 0.1.18 - in terminal I entered "make" on the command line where my samtools directory is and it seemed to be successful bc I could see the executable. When I attempt to enter it again on the command line along with my option, bash tells me that the command is not found. I aslo tried entering ./samtools instead of samtools and I recieved a "no such file or directory"

How can I fix this problem?

Thanks

[rbagnall]

Most likely it has not been added to your perl path (which means that perl cannot find the samtools application). To test this, open terminal and type:

which samtools

and this should display the path to the installation of samtools; e.g.

/Users/richardb/Richard/MY_PROJECTS/NGS/Applications/Samtools-0.1.8/samtools

if not, then you need to add samtools to your path.

[maubp]

Putting the binary on your $PATH is the easiest solution. Personally I edit my bash profile to add the directory $HOME/bin, in your case something like /Users/neophte/bin, and then move or copy the samtools binary (and other tools) to this /Users/neophte/bin/ directory.

Or, always call samtools with a full path, e.g.

/Users/neophte/downloads/samtools-0.1.18/samtools view ...

Note that when you do ./samtools the dot is Unix shorthand for the current directory.

[neophte]

thanks all for your suggestions - it worked!