In order to solve the problem, I now try to install mysql pdo

docker-php-ext-install

As noted in the readme file of the php image.

But my call failed, description:

Libraries have been installed in:
   /usr/src/php/ext/mysqli/modules

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,--rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------

Build complete.
Don't forget to run 'make test'.

Installing shared extensions:     /usr/local/lib/php/extensions/no-debug-non-zts-20131226/
Installing header files:           /usr/local/include/php/
find . -name *.gcno -o -name *.gcda | xargs rm -f
find . -name *.lo -o -name *.o | xargs rm -f
find . -name *.la -o -name *.a | xargs rm -f 
find . -name *.so | xargs rm -f
find . -name .libs -a -type d|xargs rm -rf
rm -f libphp.la       modules/* libs/*
+ cd /usr/src/php/ext/mysqlnd
+ phpize
Cannot find config.m4. 
Make sure that you run '/usr/local/bin/phpize' in the top level source directory of the module

ERROR: Service 'phlaconapp' failed to build: The command '/bin/sh -c docker-php-ext-install mysqli mysqlnd pdo pdo_mysql zip' returned a non-zero code: 1

This is my docker-compose.yml:

phlaconapp:
    hostname: phaclonapp
    dockerfile: Dockerfile
    build: ./
    ports:
        - "1080:80"
        - "1043:433"
    environment:
        TERM: xterm-color
        ENVIRONMENT: dev
    volumes:
        - ./:/var/www/html/
    links:
        - mysql
mysql:
    image: mysql:5.6
    volumes:
        - ./docker/mysql.d:/etc/mysql/conf.d
    ports: ["3306:3306"]
    environment:
        MYSQL_ROOT_PASSWORD: 'root'

This is my Dockerfile:

FROM php:5.6-apache

RUN php -r "copy('https://getcomposer.org/installer', 'composer-setup.php');" && 
    php -r "if (hash_file('SHA384', 'composer-setup.php') === '070854512ef404f16bac87071a6db9fd9721da1684cd4589b1196c3faf71b9a2682e2311b36a5079825e155ac7ce150d') { echo 'Installer verified'; } else { echo 'Installer corrupt'; unlink('composer-setup.php'); } echo PHP_EOL;" && 
    php composer-setup.php && 
    php -r "unlink('composer-setup.php');"


RUN apt-get update && 
    apt-get install vim git -y
RUN docker-php-ext-install mysqli mysqlnd pdo pdo_mysql zip 

RUN  cd /  && 
    git clone --depth=1 git://github.com/phalcon/cphalcon.git && 
    cd cphalcon/build && 
    ./install

RUN echo "extension=phalcon.so" > /usr/local/etc/php/conf.d/phalcon.ini
RUN a2enmod rewrite

And running docker-compose build will not complete.