Qa release

.gitmodules

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+[submodule "Galaxy_Middleware_API"]
+	path = Galaxy_Middleware_API
+	url = https://github.com/madgik/Galaxy_Middleware_API.git

Deployment-exareme/exareme/Exareme-Docker/Dockerfile

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+FROM alpine:3.6
+MAINTAINER Sofia Karvounari <[email protected]>
+
+# Here we install GNU libc (aka glibc) and set C.UTF-8 locale as default.
+RUN ALPINE_GLIBC_BASE_URL="https://github.com/sgerrand/alpine-pkg-glibc/releases/download" && \
+    ALPINE_GLIBC_PACKAGE_VERSION="2.23-r2" && \
+    ALPINE_GLIBC_BASE_PACKAGE_FILENAME="glibc-$ALPINE_GLIBC_PACKAGE_VERSION.apk" && \
+    ALPINE_GLIBC_BIN_PACKAGE_FILENAME="glibc-bin-$ALPINE_GLIBC_PACKAGE_VERSION.apk" && \
+    ALPINE_GLIBC_I18N_PACKAGE_FILENAME="glibc-i18n-$ALPINE_GLIBC_PACKAGE_VERSION.apk" && \
+    apk add --no-cache --virtual=build-dependencies wget ca-certificates && \
+    wget \
+        "$ALPINE_GLIBC_BASE_URL/$ALPINE_GLIBC_PACKAGE_VERSION/$ALPINE_GLIBC_BASE_PACKAGE_FILENAME" \
+        "$ALPINE_GLIBC_BASE_URL/$ALPINE_GLIBC_PACKAGE_VERSION/$ALPINE_GLIBC_BIN_PACKAGE_FILENAME" \
+        "$ALPINE_GLIBC_BASE_URL/$ALPINE_GLIBC_PACKAGE_VERSION/$ALPINE_GLIBC_I18N_PACKAGE_FILENAME" && \
+    apk add --allow-untrusted --no-cache \
+        "$ALPINE_GLIBC_BASE_PACKAGE_FILENAME" \
+        "$ALPINE_GLIBC_BIN_PACKAGE_FILENAME" \
+        "$ALPINE_GLIBC_I18N_PACKAGE_FILENAME" && \
+    /usr/glibc-compat/bin/localedef --force --inputfile POSIX --charmap UTF-8 C.UTF-8 || true && \
+    echo "export LANG=C.UTF-8" > /etc/profile.d/locale.sh && \
+    apk del glibc-i18n && \
+    apk del build-dependencies && \
+    rm \
+        "$ALPINE_GLIBC_BASE_PACKAGE_FILENAME" \
+        "$ALPINE_GLIBC_BIN_PACKAGE_FILENAME" \
+        "$ALPINE_GLIBC_I18N_PACKAGE_FILENAME"
+
+ENV LANG=C.UTF-8
+
+########################################################
+# Install Java (Shamelessly copy pasted from develar/java,
+# https://github.com/develar/docker-java/blob/master/Dockerfile)
+#
+# LSC: Updated for new URLs schemes on the Oracle website.
+ENV JAVA_VERSION_MAJOR=8 \
+    JAVA_VERSION_MINOR=141 \
+    JAVA_VERSION_BUILD=15 \
+    JAVA_VERSION_HASH=336fa29ff2bb4ef291e347e091f7f4a7 \
+    JAVA_PACKAGE=server-jre \
+    JAVA_HOME=/jre \
+    PATH=${PATH}:/jre/bin \
+    LANG=C.UTF-8
+
+# about nsswitch.conf - see https://registry.hub.docker.com/u/frolvlad/alpine-oraclejdk8/dockerfile/
+    #/usr/glibc/usr/bin/ldconfig /lib /usr/glibc/usr/lib && \
+
+RUN apk add --update curl ca-certificates && \
+        cd /tmp && \
+    echo 'hosts: files mdns4_minimal [NOTFOUND=return] dns mdns4' >> /etc/nsswitch.conf && \
+    curl -jksSLH "Cookie: oraclelicense=accept-securebackup-cookie" \
+        "http://download.oracle.com/otn-pub/java/jdk/${JAVA_VERSION_MAJOR}u${JAVA_VERSION_MINOR}-b${JAVA_VERSION_BUILD}/${JAVA_VERSION_HASH}/${JAVA_PACKAGE}-${JAVA_VERSION_MAJOR}u${JAVA_VERSION_MINOR}-linux-x64.tar.gz" \
+        | gunzip -c - | tar -xf - && \
+    apk del curl ca-certificates && \
+    mv jdk1.${JAVA_VERSION_MAJOR}.0_${JAVA_VERSION_MINOR}/jre /jre && \
+    rm /jre/bin/jjs && \
+    rm /jre/bin/keytool && \
+    rm /jre/bin/orbd && \
+    rm /jre/bin/pack200 && \
+    rm /jre/bin/policytool && \
+    rm /jre/bin/rmid && \
+    rm /jre/bin/rmiregistry && \
+    rm /jre/bin/servertool && \
+    rm /jre/bin/tnameserv && \
+    rm /jre/bin/unpack200 && \
+    rm /jre/lib/ext/nashorn.jar && \
+    rm /jre/lib/jfr.jar && \
+    rm -rf /jre/lib/jfr && \
+    rm -rf /jre/lib/oblique-fonts && \
+    rm -rf /tmp/* /var/cache/apk/*
+
+# Some extra python libraries for the mip-algorithms, which needs to be
+# compiled by hand
+ADD files/requirements.txt /root/requirements.txt
+RUN apk add --update py-psycopg2 py-pip ca-certificates gcc musl-dev python-dev lapack-dev g++ gfortran && \
+    pip install -r /root/requirements.txt && \
+    pip install scipy==1.2.1 scikit-learn==0.20.3 && \
+    pip install liac-arff && \
+    apk del py-pip ca-certificates gcc musl-dev python-dev lapack-dev gfortran && \
+    rm -rf /tmp/* /var/cache/apk/*
+
+# Runtime dependencies for Exareme
+RUN apk add --update rsync curl bash jq python py-requests lapack --no-cache procps && \
+    rm -rf /tmp/* /var/cache/apk/*
+
+
+# Add Exareme
+ADD src/exareme/exareme-distribution/target/exareme /root/exareme
+
+# Add the algorithms
+ADD src/mip-algorithms /root/mip-algorithms
+
+# Exareme configuration, ssh keys and so on
+# This has to be done after copying in the algorithms and exareme, as some
+# files are placed in folders created by those two steps.
+ADD files/java.sh /etc/profile.d/java.sh
+RUN chmod 755 /etc/profile.d/java.sh
+ADD files/root /root
+RUN chmod -R 755 /root/exareme/*.py /root/exareme/*.sh
+
+EXPOSE 9090
+EXPOSE 22
+
+ENV USER=root
+WORKDIR /root/exareme
+
+CMD ["/bin/bash","bootstrap.sh"]
+# While debugging
+#ENTRYPOINT /bin/sh

Deployment-exareme/exareme/Exareme-Docker/README.md

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+# Docker container for Exareme
+
+This project creates a Docker image for running Exareme. It has been developed on Ubuntu 16.04 LTS and not tested on other platforms.
+
+## Build procedure
+
+1. Install build requirements
+  ```
+  sudo apt-get install -y git maven curl python python-apsw jq
+  sudo apt-get install -y python-dev build-essential python-pip libblas-dev liblapack-dev libatlas-base-dev gfortran
+  ```
+
+2. Clone the sources and build Exareme
+  ```
+  git clone -b mip https://github.com/madgik/exareme.git src/exareme
+  (cd src/exareme && mvn clean install)
+  ```
+
+3. Retrieve the MIP Algorithms
+  ```
+  git clone https://github.com/madgik/mip-algorithms src/mip-algorithms
+  ```
+
+4. Building the Docker image
+  ```
+  docker build -t hbpmip/exareme .
+  ```

Deployment-exareme/exareme/Exareme-Docker/files/java.sh

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+export JAVA_VERSION_MAJOR=8
+export JAVA_VERSION_MINOR=141
+export JAVA_VERSION_BUILD=15
+export JAVA_VERSION_HASH=336fa29ff2bb4ef291e347e091f7f4a7
+export JAVA_PACKAGE=server-jre
+export JAVA_HOME=/jre
+export PATH=${PATH}:/jre/bin
+export LANG=C.UTF-8

Deployment-exareme/exareme/Exareme-Docker/files/requirements.txt

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+apsw==3.9.2-r1
+NumPy==1.16.3
+titus
+