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I have a project that doesn't use autotools, but has a Makefile which I run to build the code. This make file is run from within in a shell script. I have imported the project in eclipse, but I can't seem to run the shell script (Something like Ctrl + B to Make or add one of the Make targets viz., make all or make install).

Is there a way I can do this?

Bharath
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You can specify a script to build your project in Project Properties -> C/C++ Build -> Build Command -> Builder Settings.

You can uncheck Use default build command and specify yours (e.g. make all, make install or bash make_all.sh). Or you can leave the default build command (it must be make) and in tab Behaviour specify targets.

But before you should have imported your project Makefile Project with Existing Code.

Artem Bliednov
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Don't use Eclipse if you are using Make tools in the same project. Eclipse brings you some tools for project compiling, etc. that you already have with Make/Automake.

ibi0tux
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