add Docker support for Alpine Linux

docker/Dockerfile.alpine

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+#########################################################################################
+#
+# P R O D U C T I O N    R E A D Y
+#
+# Docker container fully based on Alpine Linux: contained PLAST software compiled
+# using native Alpine c/c++ tools.
+#
+#########################################################################################
+#
+# == Docker build command:
+#
+#    docker build -f Dockerfile.alpine -t plast_alpine_machine .
+#
+# == Running a PLAST job
+#
+#    docker run --rm -i -t plast_alpine_machine <args>
+#
+#    where <args> are the PLAST command-line arguments.
+#    See https://plast.inria.fr/user-guide/plast-command-line-arguments/
+#
+# == Sample PLAST job with provided data
+#
+#    docker run --rm -i -t -v $PWD:/tmp plast_alpine_machine -p plastp -i /opt/plastbinary/db/query.fa -d /opt/plastbinary/db/query.fa -o /tmp/test.out -a 4
+#
+#    -> you should have a 'test.out' file when PLAST job is done.
+#
+#    This command-line line explained:
+#
+#    docker run                            [1]
+#       --rm                               [2]
+#       -i -t                              [3]
+#       -v $PWD:/tmp                       [4]
+#       plast_machine                      [5] 
+#       -p plastp                          [6]
+#       -i /opt/plastbinary/db/query.fa    [7] 
+#       -d /opt/plastbinary/db/tursiops.fa [8]
+#       -o /tmp/test.out                   [9]
+#       -a 4                               [10]
+#
+#       [1]-[5]: Docker arguments
+#       [6]-[10]: PLAST arguments
+#
+#       [1]: start Docker container
+#       [2]: destroy container when Docker finishes
+#            (it does NOT delete the 'plast_machine' image)
+#       [3]: start an interactive job 
+#            (for instance, you'll see messages on stdout, if any)
+#       [4]: mount a volume. This is required to get the results from PLAST.
+#            Here, we say that current local directory will be viewed as '/tmp'
+#            from the inside of the container. 
+#       [5]: tell Docker which image to start: the 'plast_machine' of course.
+#       [6]: run a plastp job, i.e. protein query vs. protein reference bank
+#       [7]: the query; this file is provided inside the container.
+#       [8]: the reference bank; this file is provided inside the container.
+#       [9]: the result file. 
+#            Created within the '/tmp' directory inside the container, this file
+#            will be available in the current local directory, thanks to argument [4].
+#       [10]: request to use up to 4 threads
+#            (adapt the value to your computer!)
+#
+#########################################################################################
+
+FROM alpine:3.6
+# (image size after: 4Mb)
+
+# who to blame?
+MAINTAINER Patrick Durand [email protected]
+
+# ###
+#     Package installation and configuration
+#
+RUN apk update && \
+    apk add --no-cache libstdc++ && \
+    mkdir -p /opt
+# (image size after: 6.5Mb)
+
+# ###
+#     PLAST tarball is supposed to be located in this directory.
+#
+ENV PLAST_VERSION=2.3.2
+ENV PLAST_PACKAGE=plastbinary_v${PLAST_VERSION}-Alpine
+COPY ${PLAST_PACKAGE}.tar.gz /opt
+
+# ###
+#     PLAST installation.
+#
+RUN cd /opt \
+    && gunzip ${PLAST_PACKAGE}.tar.gz \
+    && tar -xf ${PLAST_PACKAGE}.tar \
+    && rm -f ${PLAST_PACKAGE}.tar \
+    && mv ${PLAST_PACKAGE} plastbinary 
+# (image size after: 9.6Mb)
+
+# ###
+#     Start a GATB-Tool. See "run-tool.sh" header for more information.
+#
+ENTRYPOINT ["/opt/plastbinary/plast"]
+

docker/Dockerfile.alpine-compiler

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+#########################################################################################
+#
+# P R O D U C T I O N    R E A D Y
+#
+# Docker container based on Alpine Linux. It aims at compiling PLAST software using 
+# Alpine c/c++ compiler.
+#
+#########################################################################################
+#
+# == Docker build command:
+#
+#    docker build -f Dockerfile.alpine-compiler -t plast_alpine_compiler .
+#
+# == Docker run command:
+#
+#    see companion scripts "build.sh" to review how to use this Alpine c/c++ complier.
+#
+#########################################################################################
+
+# Base image to compile PLAST using an Alpine Linux OS.
+# JDK is required since PLAST contains JNI interface, natively.
+# JDK is required to compile PLAST source code... however, it is not to run PLAST binary.
+# Alpine/JDK8 Docker from: https://hub.docker.com/r/frolvlad/alpine-oraclejdk8/
+FROM frolvlad/alpine-oraclejdk8:full
+
+# who to blame?
+MAINTAINER Patrick Durand [email protected]
+
+# ###
+#
+# Package installation and configuration:
+#
+#     1. We need libc and libc++ to compile PLAST
+#     2. We also need cmake, make and c/c++ compiler
+#     3. We need perl (used by cmake to get current build date)
+#     4. We need bash (compile script) and curl (to get tarballs from Github)
+#
+RUN apk update && \
+    apk add --no-cache \
+    bash \
+    curl \
+    perl \
+    cmake make g++
+    #make cmake gcc g++ libstdc++ libgcc 
+
+# Add the build script
+COPY build.sh /usr/bin
+
+# Fix: ensure script has exec permission
+RUN chmod +x /usr/bin/build.sh
+
+# Run this container as non-root
+#   testing machine: use pdurand account
+#   production machine: use Jenkins account
+RUN adduser -D -H -u 502 pdurand
+RUN adduser -D -H -u 1000 ci
+# Note: we do not use Docker 'USER' command here. Instead, use "--user xxx"
+# with "docker run" command.
+
+# ###
+#     Start to make a PLAST Tool. See "build.sh" header for more information.
+#
+ENTRYPOINT ["/usr/bin/build.sh"]
+

docker/README.md

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+# Introduction
+
+This directory contains Docker material aims at creating a PLAST Docker container.
+
+# CentOS container
+
+Genscale Team uses a CentOS 6 Linux system to compile and to test the PLAST software.
+
+As a consequence, we first designed a Dockerfile relying on that OS. 
+
+You simply create the Docker image as follows:
+
+    docker build -f Dockerfile -t plast_machine .
+
+Image size is 230 Mb.
+
+Then to run PLAST jobs using that container, refer to the header of Dockerfile.
+
+# Alpine Linux container
+
+In order to provide a more compact version of the PLAST Docker container, we designed another Dockerfile to use the compact Alpine Linux system.
+
+For that purpose, we actually made two Dockerfiles:
+
+* Dockerfile.alpine-compiler: use to compile PLAST source code into Alpine-based binary
+* Dockerfile.alpine: use to package the previous binary into a ready-to-use PLAST job machine
+
+So, you create the PLAST machine as follows:
+
+    docker build -f Dockerfile.alpine-compiler -t plast_alpine_compiler .
+    docker run --rm -i -t -v $PWD:/tmp plast_alpine_compiler \
+            "plast-library;plastbinary;plast_source;2.3.2"
+    docker build -f Dockerfile.alpine -t plast_alpine_machine .
+
+You'll end up with a very, very compact PLAST machine sizing only 9.6 Mb!
+
+To use that Docker container, please refer to the header of Dockerfile.alpine
+
+