restructure docker files to allow multiple

dockerfiles/api/Dockerfile

@@ -0,0 +1,61 @@
+FROM httpd:2.4.12
+
+# MG-RAST dependencies
+RUN apt-get update && apt-get install -y \
+  git-core \
+  libpq-dev \
+  make \
+  curl \
+  perl-modules \
+  liburi-perl \
+  libwww-perl \
+  libjson-perl \
+  libdbi-perl \
+  libdbd-mysql-perl \
+  libdbd-pg-perl \
+  libdigest-md5-perl \
+  libfile-slurp-perl \
+  libhtml-strip-perl \
+  liblist-moreutils-perl \
+  libcache-memcached-perl \
+  libhtml-template-perl \
+  libdigest-md5-perl \
+  libdigest-md5-file-perl \
+  libdatetime-perl \
+  liblist-allutils-perl \
+  libposix-strptime-perl \
+  libuuid-tiny-perl
+
+
+RUN mkdir -p /var/log/httpd/api.metagenomics/ && \
+  cd / && \
+  git clone -b api https://github.com/MG-RAST/MG-RAST.git && \
+  cd /MG-RAST && \
+  make
+
+# pipeline dependencies
+RUN apt-get install -y \
+  python-dev \
+  python-pip \
+  libtemplate-perl
+
+RUN pip install gspread xlrd openpyxl lepl
+
+RUN cd / && git clone https://github.com/MG-RAST/pipeline.git
+
+
+RUN mkdir -p /sites/1/ && \
+  cd /sites/1/ && \
+  ln -s /MG-RAST/
+
+# Configuration in mounted directory
+RUN cd /MG-RAST/conf && ln -s /api-server-conf/Conf.pm && \
+  cd /pipeline/conf && ln -s /api-server-conf/PipelineAWE_Conf.pm
+
+# m5nr blast files in mounted dir
+RUN mkdir -p /m5nr && \
+  ln -s /api-server-data/20100309 /m5nr/20100309 && \
+  ln -s /api-server-data/20131215 /m5nr/20131215
+
+# Execute:
+# /usr/local/apache2/bin/httpd -DFOREGROUND -f /MG-RAST/conf/httpd.conf