Add docker support

Author: AntonPetrov

Dockerfile

@@ -0,0 +1,68 @@
+FROM centos:6.6
+
+RUN yum install -y \
+    curl \
+    gcc \
+    git \
+    httpd \
+    httpd-devel \
+    libaio \
+    nc.x86_64 \
+    openssl \
+    openssl-devel \
+    tar \
+    unzip \
+    zlib-devel
+
+RUN mkdir /rfam
+RUN mkdir /rfam/local
+
+ENV LOC /rfam/local
+
+# Install Python
+# NOTE: Python-2.7.11 and python-2.7.11 are DIFFERENT folders, the former contains the sources, the later - binaries
+RUN \
+    cd $LOC && \
+    curl -OL http://www.python.org/ftp/python/2.7.11/Python-2.7.11.tgz && \
+    tar -zxvf Python-2.7.11.tgz && \
+    cd Python-2.7.11 && \
+    PREFIX=$LOC/python-2.7.11/ && \
+    export LD_RUN_PATH=$PREFIX/lib && \
+    ./configure --prefix=$PREFIX  --enable-shared && \
+    make && \
+    make install && \
+    cd $LOC && \
+    rm -Rf Python-2.7.11 && \
+    rm Python-2.7.11.tgz
+
+# Install virtualenv
+RUN \
+    cd $LOC && \
+    curl -OL  https://pypi.python.org/packages/source/v/virtualenv/virtualenv-15.0.0.tar.gz && \
+    tar -zxvf virtualenv-15.0.0.tar.gz && \
+    cd virtualenv-15.0.0 && \
+    $LOC/python-2.7.11/bin/python setup.py install && \
+    cd $LOC && \
+    rm -Rf virtualenv-15.0.0.tar.gz && \
+    rm -Rf virtualenv-15.0.0
+
+# Create virtual environment
+RUN \
+    cd $LOC && \
+    mkdir virtualenvs && \
+    cd virtualenvs && \
+    $LOC/python-2.7.11/bin/virtualenv rfam-production --python=$LOC/python-2.7.11/bin/python
+
+# Define container environment variables
+ENV PYTHONPATH /rfam/rfam-production
+
+# Install Python requirements
+ADD requirements.txt $RFAM_PRODUCTION
+RUN \
+    source $LOC/virtualenvs/rfam-production/bin/activate && \
+    pip install -r $RFAM_PRODUCTION/requirements.txt
+
+COPY entrypoint.sh /entrypoint.sh
+RUN chmod 700 entrypoint.sh
+
+ENTRYPOINT ["/entrypoint.sh"]

README.md

@@ -15,6 +15,23 @@ and validation.
 * **Validation:** Data validation scripts
 * **Utils:** Support modules/utilities
 
+### Using with Docker
+
+* build container
+  ```
+  docker build -t rfam-production .
+  ```
+
+* open bash interactive shell
+  ```
+  docker run -v `pwd`:/rfam/rfam-production -it rfam-production bash
+  ```
+
+* run a command inside the container
+  ```
+  docker run -v `pwd`:/rfam/rfam-production -it rfam-production python scripts/export/rfam_xml_dumper.py --out /rfam --type R
+  ```
+
 ### Installation
 
 ```

entrypoint.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+source $LOC/virtualenvs/rfam-production/bin/activate
+cd $PYTHONPATH
+exec "$@"