how to run alias using bash -c from IDEA
The reason of your failure is that myapp is evaluated by bash at the time of the line evaluation, i.e. before its definition.
I suggest you to avoid aliases for this purpose (I can't find any easy method with aliases).

Here is a simple method.
If you don't have already one, create a personnal directory for all your
binaries and shell scripts:

$ mkdir ~/bin


Add this new directory within your shell standard PATH:

PATH=${PATH}:~/bin
export PATH


Create a new shell script to fire your application with all the
required arguments:

$ cd ~/bin
$ cat &gt;myapp.sh &lt;&lt;eof
/somepath/app -arg1 -arg2
eof
$ make myapp


check that it is working from your actual environment:

$ myapp


Then call it from IDEA:

Program: myapp


check that it is working from within IDEA.