<commit_before># RStudio container used for Galaxy RStudio Integration
#
# VERSION       0.1.0

FROM debian:squeeze

MAINTAINER <NAME> <<EMAIL>>

ENV DEBIAN_FRONTEND noninteractive
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US.UTF-8


# Ensure cran is available
RUN (echo "deb http://cran.mtu.edu/bin/linux/debian squeeze-cran3/" >> /etc/apt/sources.list && \
    apt-key adv --keyserver keys.gnupg.net --recv-key 381BA480) && \
    (echo "deb-src http://http.debian.net/debian squeeze main" >> /etc/apt/sources.list && \
    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9) && \
    apt-get -qq update && \
    apt-get install --no-install-recommends -y apt-transport-https \
        locales r-base r-base-dev dpkg wget psmisc libssl0.9.8 procps sudo \
        libcurl4-openssl-dev curl libxml2-dev nginx python python-pip net-tools \
        lsb-release tcpdump unixodbc unixodbc-dev libmyodbc odbcinst odbc-postgresql \
        texlive-latex-base texlive-extra-utils texlive-fonts-recommended texlive-latex-recommended && \
    pip install bioblend argparse && \
    apt-get autoremove -y  && \
    apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN echo 'en_US.UTF-8 UTF-8' >> /etc/locale.gen
RUN DEBIAN_FRONTEND=noninteractive dpkg-reconfigure locales

# Build specific
ENV RSTUDIO_VERSION 0.99.891

# Install rstudio-server
RUN wget http://download2.rstudio.org/rstudio-server-${RSTUDIO_VERSION}-amd64.deb && \
    dpkg -i rstudio-server-0.98.${RSTUDIO_VERSION}-amd64.deb && \
    rm /rstudio-server-0.98.${RSTUDIO_VERSION}-amd64.deb

ADD rsession.conf /etc/rstudio/rsession.conf

# Install packages
COPY ./packages.R /tmp/packages.R
RUN Rscript /tmp/packages.R

# ENV variables to replace conf file from Galaxy
ENV DEBUG=false \
    GALAXY_WEB_PORT=10000 \<commit_msg>Updates for newer RStudio image<commit_after># RStudio container used for Galaxy RStudio Integration
#
# VERSION       0.1.0

FROM debian:squeeze

MAINTAINER <NAME> <<EMAIL>>

ENV DEBIAN_FRONTEND=noninteractive \
    LANG=en_US.UTF-8 \
    LANGUAGE=en_US.UTF-8 \
    LC_ALL=en_US.UTF-8

# Ensure cran is available
RUN (echo "deb http://cran.mtu.edu/bin/linux/debian squeeze-cran3/" >> /etc/apt/sources.list && \
    apt-key adv --keyserver keys.gnupg.net --recv-key 381BA480) && \
    (echo "deb-src http://http.debian.net/debian squeeze main" >> /etc/apt/sources.list && \
    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9) && \
    apt-get -qq update && \
    apt-get install --no-install-recommends -y apt-transport-https \
        locales r-base r-base-dev dpkg wget psmisc libssl0.9.8 procps sudo \
        libcurl4-openssl-dev curl libxml2-dev nginx python python-pip net-tools \
        lsb-release tcpdump unixodbc unixodbc-dev libmyodbc odbcinst odbc-postgresql \
        texlive-latex-base texlive-extra-utils texlive-fonts-recommended \
        texlive-latex-recommended libapparmor1 libedit2 && \
    pip install bioblend argparse && \
    apt-get autoremove -y  && \
    apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN locale-gen en_US.UTF-8 && dpkg-reconfigure locales

# Build specific
ENV RSTUDIO_VERSION 0.99.891

# Install rstudio-server
RUN wget http://download2.rstudio.org/rstudio-server-${RSTUDIO_VERSION}-amd64.deb && \
    dpkg -i rstudio-server-${RSTUDIO_VERSION}-amd64.deb && \
    rm /rstudio-server-${RSTUDIO_VERSION}-amd64.deb

ADD rsession.conf /etc/rstudio/rsession.conf

# Install packages
COPY ./packages.R /tmp/packages.R
RUN Rscript /tmp/packages.R

# ENV variables to replace conf file from Galaxy
ENV DEBUG=false \
    GALAXY_WEB_PORT=10000 \
{'fraction_non_alphanumeric': 0.1256544502617801, 'fraction_numerical': 0.024800220446403967, 'mean_word_length': 3.1016949152542375, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 19, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '39596', 'n_tokens_mistral': 1415, 'n_tokens_neox': 1323, 'n_words': 294}