<commit_before># Galaxy - Bingomics
#
# VERSION       Galaxy-central

FROM chambm/docker-galaxy-stable

MAINTAINER <NAME>, <EMAIL>

# Install various tool and development requirements
# 1. Add R-dev PPA and its public key (then 'apt-get update')
# 2. Install linuxbrew requirements
# 3. Install python-h5py (for mz5 support in Galaxy)
# 4. Install R-3.2 from R-dev PPA
# 5. Cleanup
RUN codename=$(lsb_release -c -s) && \
    echo "deb http://mirrors.nics.utk.edu/cran/bin/linux/ubuntu $codename/" | tee -a /etc/apt/sources.list && \
    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 && \
    echo "deb http://ppa.launchpad.net/marutter/rdev/ubuntu $codename main" | tee -a /etc/apt/sources.list.d/marutter-rdev-$codename.list && \
    apt-get -qq update && \
    apt-get install -y --no-install-recommends r-base cabextract build-essential curl git m4 ruby texinfo libbz2-dev libcurl4-openssl-dev libexpat-dev libncurses-dev zlib1g-dev libhdf5-dev python-h5py libreadline-dev && \
    sudo -u galaxy ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/linuxbrew/go/install)" && \
    echo export PATH=$PATH:/home/galaxy/.linuxbrew/bin >> /home/galaxy/.bashrc && \
    apt-get purge -y software-properties-common && \
    apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

### WINE support currently not working
# Add i386 architecture and run apt-get update
# Install wine and xvfb (console frame buffer for X11)
# Download winetricks from their site and make it executable
#RUN dpkg --add-architecture i386 && apt-get -qq update && \
#    apt-get install -y --no-install-recommends wine xvfb && \
#    wget https://raw.githubusercontent.com/Winetricks/winetricks/master/src/winetricks && chmod ugo+rx winetricks && chown galaxy:galaxy winetricks && mv winetricks /usr/local/bin && \
#    apt-get purge -y software-properties-common && \
#    apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Install BioConductor and proBAMr
RUN R --vanilla -e 'source("http://bioconductor.org/biocLite.R"); biocLite(ask=F)' && \
    R --vanilla -e 'source("http://bioconductor.org/biocLite.R"); biocLite(c("RGalaxy", "proBAMr"), ask=F)'

# Install Bingomics tools into Galaxy
RUN add-tool-shed --url 'http://testtoolshed.g2.bx.psu.edu/' --name 'Test Tool Shed' && \
    install-repository "--url http://testtoolshed.g2.bx.psu.edu/ -o galaxyp --name myrimatch" \
                       "--url http://testtoolshed.g2.bx.psu.edu/ -o galaxyp --name idpqonvert" \
                       "--url http://testtoolshed.g2.bx.psu.edu/ -o galaxyp --name idpassemble" \
                       "--url http://testtoolshed.g2.bx.psu.edu/ -o galaxyp --name idpquery" \
                       "--url http://testtoolshed.g2.bx.psu.edu/ -o galaxyp --name msconvert"

# The following commands will be executed as user galaxy
USER galaxy

# BASH_ENV tells bash what to do for non-interactive logins
ENV PATH=$PATH:/home/galaxy/.linuxbrew/bin BASH_ENV=/home/galaxy/.bashrc

# Install planemo (will be installed in linuxbrew's bin directory)
RUN brew tap galaxyproject/tap && brew install planemo --HEAD

ENV GALAXY_CONFIG_BRAND="Bingomics" \
    GALAXY_CONFIG_JOB_WORKING_DIRECTORY=/export/galaxy-cluster/job_working_directory \
    GALAXY_CONFIG_FILE_PATH=/export/galaxy-central/database/files \
    GALAXY_CONFIG_NEW_FILE_PATH=/export/galaxy-central/database/files \
    GALAXY_CONFIG_TEMPLATE_CACHE_PATH=/galaxy-central/database/compiled_templates \
    GALAXY_CONFIG_CITATION_CACHE_DATA_DIR=/galaxy-central/database/citations/data \
    GALAXY_CONFIG_CLUSTER_FILES_DIRECTORY=/export/galaxy-cluster/pbs \
    GALAXY_CONFIG_FTP_UPLOAD_DIR=/export/galaxy-central/database/ftp \
    GALAXY_CONFIG_FTP_UPLOAD_SITE=192.168.33.10 \
    ENABLE_TTS_INSTALL=True

WORKDIR /galaxy-central

# set WINEPREFIX and WINEARCH for galaxy user
ENV WINEPREFIX=$HOME/.wine32 WINEARCH=win32

#RUN xvfb-run winetricks -q winxp vcrun2005 win7 vcrun2008 vcrun2010 vcrun2012 vcrun2013
#RUN xvfb-run winetricks -q dotnet35sp1 dotnet40

<commit_msg>- added libxml2 to apt install list (required by at least one BioConductor package) - added msgfplus, psm_to_sam, sam_to_bam, and sam_merge tools to the install-repository list<commit_after># Galaxy - Bingomics
#
# VERSION       Galaxy-central

FROM chambm/docker-galaxy-stable

MAINTAINER <NAME>, <EMAIL>

# Install various tool and development requirements
# 1. Add R-dev PPA and its public key (then 'apt-get update')
# 2. Install linuxbrew requirements
# 3. Install python-h5py (for mz5 support in Galaxy)
# 4. Install R-3.2 from R-dev PPA
# 5. Cleanup
RUN codename=$(lsb_release -c -s) && \
    echo "deb http://mirrors.nics.utk.edu/cran/bin/linux/ubuntu $codename/" | tee -a /etc/apt/sources.list && \
    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 && \
    echo "deb http://ppa.launchpad.net/marutter/rdev/ubuntu $codename main" | tee -a /etc/apt/sources.list.d/marutter-rdev-$codename.list && \
    apt-get -qq update && \
    apt-get install -y --no-install-recommends r-base cabextract build-essential curl git m4 ruby texinfo libbz2-dev libcurl4-openssl-dev libxml2-dev libexpat-dev libncurses-dev zlib1g-dev libhdf5-dev python-h5py libreadline-dev && \
    sudo -u galaxy ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/linuxbrew/go/install)" && \
    echo export PATH=$PATH:/home/galaxy/.linuxbrew/bin >> /home/galaxy/.bashrc && \
    apt-get purge -y software-properties-common && \
    apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

### WINE support currently not working
# Add i386 architecture and run apt-get update
# Install wine and xvfb (console frame buffer for X11)
# Download winetricks from their site and make it executable
#RUN dpkg --add-architecture i386 && apt-get -qq update && \
#    apt-get install -y --no-install-recommends wine xvfb && \
#    wget https://raw.githubusercontent.com/Winetricks/winetricks/master/src/winetricks && chmod ugo+rx winetricks && chown galaxy:galaxy winetricks && mv winetricks /usr/local/bin && \
#    apt-get purge -y software-properties-common && \
#    apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Install BioConductor and proBAMr
RUN R --vanilla -e 'source("http://bioconductor.org/biocLite.R"); biocLite(ask=F)' && \
    R --vanilla -e 'source("http://bioconductor.org/biocLite.R"); biocLite(c("RGalaxy", "proBAMr"), ask=F)'

# Install Bingomics tools into Galaxy
RUN add-tool-shed --url 'http://testtoolshed.g2.bx.psu.edu/' --name 'Test Tool Shed' && \
    install-repository "--url http://testtoolshed.g2.bx.psu.edu/ -o galaxyp --name myrimatch" \
                       "--url http://testtoolshed.g2.bx.psu.edu/ -o galaxyp --name idpqonvert" \
                       "--url http://testtoolshed.g2.bx.psu.edu/ -o galaxyp --name idpassemble" \
                       "--url http://testtoolshed.g2.bx.psu.edu/ -o galaxyp --name idpquery" \
                       "--url http://testtoolshed.g2.bx.psu.edu/ -o galaxyp --name msconvert" \
                       "--url http://testtoolshed.g2.bx.psu.edu/ -o galaxyp --name psm_to_sam" \
                       "--url http://toolshed.g2.bx.psu.edu/ -o devteam --name sam_to_bam" \
                       "--url http://toolshed.g2.bx.psu.edu/ -o devteam --name sam_merge"

RUN install-repository "--url http://testtoolshed.g2.bx.psu.edu/ -o galaxyp --name msgfplus"

# The following commands will be executed as user galaxy
USER galaxy

# BASH_ENV tells bash what to do for non-interactive logins
ADD .bashrc /home/galaxy/.bashrc
ENV PATH=$PATH:/home/galaxy/.linuxbrew/bin BASH_ENV=/home/galaxy/.bashrc

# Install planemo (will be installed in linuxbrew's bin directory)
RUN brew tap galaxyproject/tap && brew install planemo --HEAD

ENV GALAXY_CONFIG_BRAND="Bingomics" \
    GALAXY_CONFIG_JOB_WORKING_DIRECTORY=/export/galaxy-cluster/job_working_directory \
    GALAXY_CONFIG_FILE_PATH=/export/galaxy-central/database/files \
    GALAXY_CONFIG_NEW_FILE_PATH=/export/galaxy-central/database/files \
    GALAXY_CONFIG_TEMPLATE_CACHE_PATH=/galaxy-central/database/compiled_templates \
    GALAXY_CONFIG_CITATION_CACHE_DATA_DIR=/galaxy-central/database/citations/data \
    GALAXY_CONFIG_CLUSTER_FILES_DIRECTORY=/export/galaxy-cluster/pbs \
    GALAXY_CONFIG_FTP_UPLOAD_DIR=/export/galaxy-central/database/ftp \
    GALAXY_CONFIG_FTP_UPLOAD_SITE=192.168.33.10 \
    ENABLE_TTS_INSTALL=True

WORKDIR /galaxy-central

# set WINEPREFIX and WINEARCH for galaxy user
ENV WINEPREFIX=$HOME/.wine32 WINEARCH=win32

#RUN xvfb-run winetricks -q winxp vcrun2005 win7 vcrun2008 vcrun2010 vcrun2012 vcrun2013
#RUN xvfb-run winetricks -q dotnet35sp1 dotnet40


{'fraction_non_alphanumeric': 0.12958323844226827, 'fraction_numerical': 0.01730813026645411, 'mean_word_length': 3.230732177263969, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 11, 'https://': 4, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 2, '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': '3694683', 'n_tokens_mistral': 3284, 'n_tokens_neox': 3033, 'n_words': 714}