[kmcarr]

Cool it works but not quite!!!

LOL

prompt>export PATH=$PATH:/Developer/usr/bin
prompt>make
make: *** No targets specified and no makefile found. Stop.

How do I edit the .bashrc file can I just do a "cat" or something as I don't trust my text edit to do the job properly.

What would people recommend for editing files with the correct line breaks and CR etc..

qnc,

Installing XCode puts all of the necessary development tools in /usr/bin in addition to /Developer/usr/bin so you shouldn't need to alter your $PATH variable. With XCode installed try this test (launch a new Terminal to make sure your environment is updated):

prompt> which make

It should print /usr/bin/make

As for the error you saw when trying to run make (*** No targets specified and no makefile found. Stop.) are you sure that you were in the samtools source directory? Do this:

prompt> ls -l

Is there a file named "Makefile" listed?

An easy to use and free text editor for the Mac is TextWrangler. It has the option to save text files with line endings appropriate for *nix (LF), Mac (CR) or Windows (CRLF). The default can be set via the Preferences or you can set for a given file from a pop-up at the bottom of the editing window.

Edited to add: You can also get TextWrangler from the Apple Mac App Store. If "purchase" (it's free) the app from the App store make sure to also go to the BareBones site to download the TextWrangler command line tools installer. Apps sold through the App store can not include command line tools.

[qnc]

This is great advice guys. Thanks will let you know how I get on.