run newbler v2.9 in command line

Question

[midox]

Hello,

I installed newbler but when I hit the problem: gsAssembly or runAssembly the answer is

[Midox @ Jarvis sources/454/bin /] $ runAssembly
-bash: runAssembly: command not found

(sources/454/bin/ is the path or folder installed newbler)

Is what you can tell me the command line to test newbler because on the net the commands do not work?

Thank you

Answer 1

[pld]

The problem isn't with the Newbler software, it is how you're calling the runAssembly script.

When you use a command like foo, unless it is a command defined in your bashrc/profile, the shell will search all of the places listed in your $PATH looking for foo. In other words, the shell needs to know where to find the command/program you're calling.

With normally installed programs or built in things like ls, the path is typically already updated. So you don't need to provide the location of the command. You can confirm this by running which ls, you'll see that the location of ls is known.

So, either add the path where the shell scripts the newbler assembler uses are to your environment, or you can call them by providing the directory in your path variable or make an alias. E.g. if I installed them in /usr/bin I would have to call runAssembly with /usr/bin/runAssembly.

[midox]

OK thank you