Set ENV variable in container is not working, is every under "/usr/local/bin" executed on container run?

You're correct in that items under /usr/local/bin are not automatically executed.

The Filesystem Hierarchy Standard specifies /usr/local as a "tertiary hierarchy" with its own bin, lib, &c. subdirectories, equivalent in their intent and use to the like-named directories under / or /usr but for content installed local to the machine (in practice, this means software installed without the benefit of the local distro's packaging system).

If you want a command to be executed, you need a RUN that directly or indirectly invokes it.

As for the other matters discussed as this question has morphed, consider the following:

FROM alpineENV foo=barRUN echo $foo >/tmp/foo-valueCMD cat /tmp/foo-value; echo $foo

When invoked with:

docker run -e foo=qux

...this emits as output:

barqux

...because bar is the environment variable laid down by the RUN command, whereas qux is the environment variable as it exists at the CMD command's execution.

Thus, to ensure that an environment variable is honored in configuration, it must be read and applied during the CMD's execution, not during a prior RUN stage.

Multiple problems with your repo:

First of all when using CMD in docker file, the command added after the image name in the docker run : /bin/bash will override the CMD ["/usr/local/bin/setup_php_settings"] from your Dockerfile.

Thus your setup_php_settings is never executed!You should use ENTRYPOINT i.s.o. CMD in your Dockerfile. I found good explanation here and here.

In conclusion for the Dockerfile change the CMD [...] line in:

ENTRYPOINT bash -C '/usr/local/bin/setup_php_settings';'bash'

then you can run your container with:

docker run -it -e HOST_IP=<your_ip_address> -e PHP_ERROR_REPORTING='E_ALL & ~E_STRICT' -p 80:80 --name dev-php5 mmi/dev-php55

No need to add /bin/bash at the end. Check-out test-repo for test-setup.

Secondly, in your /usr/local/bin/setup_php_settings, you should add

a2enmod rewriteservice apache2 restart

at the end, just before

source /etc/apache2/envvars && exec /usr/sbin/apache2 -DFOREGROUND`

this in order for your new settings to be applied in your web app.