<commit_before>###########################################################################
# Dugong - Scientific Linux Containers for Bioinformatic
# ======================================================
#
# Current development is led by <NAME>.
#
# Bioinformatician/Bioinformaticist at the Laboratory of Functional 
# and Structural Genomics of the Integrated Nucleus of Biotechnology 
# at the University of Mogi das Cruzes, Brazil.
# 
# Contact: <EMAIL>
# GitHub: https://github.com/fabianomenegidio
#
#
###########################################################################

FROM ubuntu:latest
MAINTAINER <NAME> <<EMAIL>>

############### Metadata
LABEL base.image="ubuntu:latest"
LABEL version="1.0"
LABEL name="Dugong"
LABEL flavour="Xfce4"
LABEL description="Scientific Linux Container"
LABEL website="https://fabianomenegidio.github.io/dugong-bioinformatics/"
LABEL repository="https://github.com/fabianomenegidio/dugong-bioinformatics"
LABEL license="https://github.com/fabianomenegidio/dugong-bioinformatics/blob/master/LICENSE"
LABEL tags="Bioinformatics"

###############  Connection ports for controlling the UI:
# VNC port:5901
# noVNC webport, connect via http://IP:6901/?password=<PASSWORD>
############### 
ENV DISPLAY :1
ENV VNC_PORT 5901
ENV NO_VNC_PORT 6901
EXPOSE $VNC_PORT $NO_VNC_PORT

ENV HOME /headless
ENV STARTUPDIR /dockerstartup
WORKDIR $HOME

############### Environment config
ENV DEBIAN_FRONTEND noninteractive
ENV NO_VNC_HOME $HOME/noVNC
ENV VNC_COL_DEPTH 24
ENV VNC_PW <PASSWORD>

############### Resolution Chromebook (change to your default resolution)
ENV VNC_RESOLUTION 1366x768

############### Add Linux Mint dependencies and update packages
RUN apt-key adv --recv-key --keyserver keyserver.ubuntu.com "<KEY>"
RUN echo "deb http://packages.linuxmint.com sarah main upstream import backport" >> /etc/apt/sources.list.d/mint.list && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
    

############### Add Xenial dependencies and update packages
RUN echo "deb mirror://mirrors.ubuntu.com/mirrors.txt xenial main restricted universe multiverse" >> /etc/apt/sources.list.d/xenial.list && \
    echo "deb mirror://mirrors.ubuntu.com/mirrors.txt xenial-updates main restricted universe multiverse" >> /etc/apt/sources.list.d/xenial.list  && \
    echo "deb mirror://mirrors.ubuntu.com/mirrors.txt xenial-backports main restricted universe multiverse"  && \
    echo "deb mirror://mirrors.ubuntu.com/mirrors.txt xenial-security main restricted universe multiverse" >> /etc/apt/sources.list.d/xenial.list

############### Add BioLinux 8 dependencies and update packages
RUN echo 'deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux' >> /etc/apt/sources.list.d/biolinux.list && \
    echo 'deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main' >> /etc/apt/sources.list.d/biolinux.list && \
    echo 'deb-src http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main' >> /etc/apt/sources.list.d/biolinux.list && \
    echo 'deb http://cran.r-project.org/bin/linux/ubuntu precise/' >> /etc/apt/sources.list.d/biolinux.list && \
    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 && \
    apt-get update && \
    apt-get install -y --allow-unauthenticated --force-yes bio-linux-keyring && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

############### Add all install scripts for further steps
ENV INST_SCRIPTS $HOME/install
ADD .config/install/ $INST_SCRIPTS/
RUN find $INST_SCRIPTS -name '*.sh' -exec chmod a+x {} +

############### Installation of essential packages and dependencies
RUN $INST_SCRIPTS/tools.sh

############### Install xvnc-server & noVNC - HTML5 based VNC viewer
RUN $INST_SCRIPTS/tigervnc.sh
RUN $INST_SCRIPTS/no_vnc.sh

############### Install Chrome Browser & Firefox
RUN $INST_SCRIPTS/firefox.sh
RUN $INST_SCRIPTS/chrome.sh
<commit_msg>Update Dockerfile<commit_after>###########################################################################
# Dugong - Scientific Linux Containers for Bioinformatic
# ======================================================
#
# Current development is led by <NAME>.
#
# Bioinformatician/Bioinformaticist at the Laboratory of Functional 
# and Structural Genomics of the Integrated Nucleus of Biotechnology 
# at the University of Mogi das Cruzes, Brazil.
# 
# Contact: <EMAIL>
# GitHub: https://github.com/fabianomenegidio
#
#
###########################################################################

FROM ubuntu:latest
MAINTAINER <NAME> <<EMAIL>>

############### Metadata
LABEL base.image="ubuntu:latest"
LABEL version="1.0"
LABEL name="Dugong"
LABEL flavour="Xfce4"
LABEL description="Scientific Linux Container"
LABEL website="https://fabianomenegidio.github.io/dugong-bioinformatics/"
LABEL repository="https://github.com/fabianomenegidio/dugong-bioinformatics"
LABEL license="https://github.com/fabianomenegidio/dugong-bioinformatics/blob/master/LICENSE"
LABEL tags="Bioinformatics"

###############  Connection ports for controlling the UI:
# VNC port:5901
# noVNC webport, connect via http://IP:6901/?password=<PASSWORD>
############### 
ENV DISPLAY :1
ENV VNC_PORT 5901
ENV NO_VNC_PORT 6901
EXPOSE $VNC_PORT $NO_VNC_PORT

ENV HOME /headless
ENV STARTUPDIR /dockerstartup
WORKDIR $HOME

############### Environment config
ENV DEBIAN_FRONTEND noninteractive
ENV NO_VNC_HOME $HOME/noVNC
ENV VNC_COL_DEPTH 24
ENV VNC_PW <PASSWORD>

############### Resolution Chromebook (change to your default resolution)
ENV VNC_RESOLUTION 1366x768

############### Add Linux Mint dependencies and update packages
RUN apt-key adv --recv-key --keyserver keyserver.ubuntu.com "<KEY>"
RUN echo "deb http://packages.linuxmint.com sarah main upstream import backport" >> /etc/apt/sources.list.d/mint.list && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
    

############### Add Xenial dependencies and update packages
RUN echo "deb mirror://mirrors.ubuntu.com/mirrors.txt xenial main restricted universe multiverse" >> /etc/apt/sources.list.d/xenial.list && \
    echo "deb mirror://mirrors.ubuntu.com/mirrors.txt xenial-updates main restricted universe multiverse" >> /etc/apt/sources.list.d/xenial.list  && \
    echo "deb mirror://mirrors.ubuntu.com/mirrors.txt xenial-backports main restricted universe multiverse"  && \
    echo "deb mirror://mirrors.ubuntu.com/mirrors.txt xenial-security main restricted universe multiverse" >> /etc/apt/sources.list.d/xenial.list

############### Add BioLinux 8 dependencies and update packages
RUN echo 'deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux' >> /etc/apt/sources.list.d/biolinux.list && \
    echo 'deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main' >> /etc/apt/sources.list.d/biolinux.list && \
    echo 'deb http://cran.r-project.org/bin/linux/ubuntu precise/' >> /etc/apt/sources.list.d/biolinux.list && \
    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 && \
    apt-get update && \
    apt-get install -y --allow-unauthenticated --force-yes bio-linux-keyring && \
    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

############### Add all install scripts for further steps
ENV INST_SCRIPTS $HOME/install
ADD .config/install/ $INST_SCRIPTS/
RUN find $INST_SCRIPTS -name '*.sh' -exec chmod a+x {} +

############### Installation of essential packages and dependencies
RUN $INST_SCRIPTS/tools.sh

############### Install xvnc-server & noVNC - HTML5 based VNC viewer
RUN $INST_SCRIPTS/tigervnc.sh
RUN $INST_SCRIPTS/no_vnc.sh

############### Install Chrome Browser & Firefox
RUN $INST_SCRIPTS/firefox.sh
RUN $INST_SCRIPTS/chrome.sh

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{'dir': 'git-commits-cleaned', 'id': '5362718', 'n_tokens_mistral': 2589, 'n_tokens_neox': 2397, 'n_words': 587}