<commit_before># Galaxy - Stable
#
# VERSION       0.1

FROM debian:wheezy

MAINTAINER <NAME>, <EMAIL>

# make sure the package repository is up to date
RUN DEBIAN_FRONTEND=noninteractive apt-get -qq update

# Set Apache User and Group
ENV APACHE_RUN_USER www-data
ENV APACHE_RUN_GROUP www-data
ENV APACHE_LOG_DIR /var/log/apache2

# Install all requirements that are recommend by the Galaxy project
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y autoconf
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y automake
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y build-essential
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y gfortran
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y cmake
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y git-core
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libatlas-base-dev
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libblas-dev
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y liblapack-dev
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y mercurial
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y subversion
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y python-dev
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y pkg-config
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y openjdk-7-jre
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y python-setuptools

# Used to get Galaxy running in Docker with Apache2 and PostgreSQL
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y postgresql
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y apache2
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libapache2-mod-xsendfile

# samtools is used to handle BAM files inside of Galaxy
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y samtools

# Load required Apache Modules
RUN a2enmod xsendfile
RUN a2enmod proxy
RUN a2enmod proxy_balancer
RUN a2enmod proxy_http
RUN a2enmod rewrite

# Download and update Galaxy to the latest stable release
RUN hg clone https://bitbucket.org/galaxy/galaxy-central/
WORKDIR /galaxy-central
RUN hg pull
RUN hg update next-stable

# Configure Galaxy to use the Tool Shed
RUN cp ~/galaxy-central/universe_wsgi.ini.sample ~/galaxy-central/universe_wsgi.ini
RUN mkdir ~/shed_tools<commit_msg>update to latest Galaxy stable release from 11.8.2014<commit_after># Galaxy - Stable
#
# VERSION       0.1

FROM debian:wheezy

MAINTAINER <NAME>, <EMAIL>

# make sure the package repository is up to date
RUN DEBIAN_FRONTEND=noninteractive apt-get -qq update

# Set Apache User and Group
ENV APACHE_RUN_USER www-data
ENV APACHE_RUN_GROUP www-data
ENV APACHE_LOG_DIR /var/log/apache2

# Install all requirements that are recommend by the Galaxy project
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y autoconf
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y automake
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y build-essential
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y gfortran
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y cmake
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y git-core
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libatlas-base-dev
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libblas-dev
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y liblapack-dev
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y mercurial
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y subversion
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y python-dev
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y pkg-config
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y openjdk-7-jre
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y python-setuptools

# Used to get Galaxy running in Docker with Apache2 and PostgreSQL
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y postgresql
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y apache2
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libapache2-mod-xsendfile

# samtools is used to handle BAM files inside of Galaxy
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y samtools

# Load required Apache Modules
RUN a2enmod xsendfile
RUN a2enmod proxy
RUN a2enmod proxy_balancer
RUN a2enmod proxy_http
RUN a2enmod rewrite

# Download and update Galaxy to the latest stable release
RUN hg clone https://bitbucket.org/galaxy/galaxy-central/
WORKDIR /galaxy-central
RUN hg pull
RUN hg update latest_2014.08.11

# Configure Galaxy to use the Tool Shed
RUN cp ~/galaxy-central/universe_wsgi.ini.sample ~/galaxy-central/universe_wsgi.ini
RUN mkdir ~/shed_tools
{'fraction_non_alphanumeric': 0.07354014598540146, 'fraction_numerical': 0.007116788321167883, 'mean_word_length': 5.165354330708661, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 7, 'https://': 2, 'lorem ipsum': 0, 'www.': 4, 'xml': 0}, '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': '4180165', 'n_tokens_mistral': 1868, 'n_tokens_neox': 1839, 'n_words': 520}