<commit_before># MG-RAST API

FROM httpd:2.4.12

# MG-RAST dependencies
RUN apt-get update && apt-get install -y \
  git-core \
  libpq-dev \
  make \
  curl \
  perl-modules \
  liburi-perl \
  libwww-perl \
  libjson-perl \
  libdbi-perl \
  libdbd-mysql-perl \
  libdbd-pg-perl \
  libdigest-md5-perl \
  libfile-slurp-perl \
  libhtml-strip-perl \
  liblist-moreutils-perl \
  libcache-memcached-perl \
  libhtml-template-perl \
  libdigest-md5-perl \
  libdigest-md5-file-perl \
  libdatetime-perl \
  liblist-allutils-perl \
  libposix-strptime-perl \
  libuuid-tiny-perl \
  libmongodb-perl \
  libfreezethaw-perl \
  libtemplate-perl \
  libclass-isa-perl

# setup sendmail
RUN DEBIAN_FRONTEND=noninteractive apt-get -y install postfix && \
  cp /usr/share/postfix/main.cf.debian /etc/postfix/main.cf && \
  pkill -9 sendmail && \
  postconf -e relayhost=[smtp.mcs.anl.gov] && \
  /etc/init.d/postfix restart && \
  exit 0

RUN mkdir -p /var/log/httpd/api.metagenomics/ && \
  cd / && \
  git clone -b api https://github.com/MG-RAST/MG-RAST.git && \
  cd /MG-RAST && \
  make && \
  cd site/CGI && \
  rm -fv metagenomics.cgi linkin.cgi m5nr.cgi m5nr_rest.cgi

# R dependencies
RUN apt-get install -y r-base r-cran-nlme r-cran-ecodist r-cran-rcolorbrewer r-cran-xml && \
  echo 'install.packages("matlab", repos = "http://cran.wustl.edu")' | R --no-save && \
  echo 'source("http://bioconductor.org/biocLite.R"); biocLite("pcaMethods"); biocLite("preprocessCore"); biocLite("DESeq")' | R --no-save<commit_msg>Update Dockerfile<commit_after># MG-RAST API

FROM httpd:2.4.12

# MG-RAST dependencies
RUN apt-get update && apt-get install -y \
  git-core \
  libpq-dev \
  make \
  curl \
  perl-modules \
  liburi-perl \
  libwww-perl \
  libjson-perl \
  libdbi-perl \
  libdbd-mysql-perl \
  libdbd-pg-perl \
  libdigest-md5-perl \
  libfile-slurp-perl \
  libhtml-strip-perl \
  liblist-moreutils-perl \
  libcache-memcached-perl \
  libhtml-template-perl \
  libdigest-md5-perl \
  libdigest-md5-file-perl \
  libdatetime-perl \
  liblist-allutils-perl \
  libposix-strptime-perl \
  libuuid-tiny-perl \
  libmongodb-perl \
  libfreezethaw-perl \
  libtemplate-perl \
  libclass-isa-perl

# setup sendmail
RUN apt-get -y install postfix && \
  cp /usr/share/postfix/main.cf.debian /etc/postfix/main.cf && \
  pkill -9 sendmail && \
  postconf -e relayhost=[smtp.mcs.anl.gov] && \
  exit 0

RUN mkdir -p /var/log/httpd/api.metagenomics/ && \
  cd / && \
  git clone -b api https://github.com/MG-RAST/MG-RAST.git && \
  cd /MG-RAST && \
  make && \
  cd site/CGI && \
  rm -fv metagenomics.cgi linkin.cgi m5nr.cgi m5nr_rest.cgi

# R dependencies
RUN apt-get install -y r-base r-cran-nlme r-cran-ecodist r-cran-rcolorbrewer r-cran-xml && \
  echo 'install.packages("matlab", repos = "http://cran.wust<EMAIL>")' | R --no-save && \
  echo 'source("http://bioconductor.org/biocLite.R"); biocLite("pcaMethods"); biocLite("preprocessCore"); biocLite("DESeq")' | R --no-save
{'fraction_non_alphanumeric': 0.15635507733691997, 'fraction_numerical': 0.007397444519166106, 'mean_word_length': 2.6683107274969173, 'pattern_counts': {'":': 0, '<': 4, '<?xml version=': 0, '>': 4, 'https://': 2, 'lorem ipsum': 0, 'www.': 2, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2102438', 'n_tokens_mistral': 1301, 'n_tokens_neox': 1222, 'n_words': 209}