<commit_before>FROM ubuntu:14.04
MAINTAINER <NAME> <<EMAIL>>

# fetchChromSizes can use mysql, wget, or FTP
RUN apt-get update && apt-get install -y \
  curl \
  wget \
  bedtools

WORKDIR /usr/local/bin

# Fetch tools from hgdownload and place in /usr/local/bin
RUN curl -SLO http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig
RUN curl -SLO http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes
RUN curl -SLO http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/hubCheck
RUN curl -SLO http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver
RUN chmod +x *

# Add local code
RUN mkdir -p /opt/TrackHubGenerator
COPY . /opt/TrackHubGenerator
WORKDIR /opt/TrackHubGenerator/python

# Install python dependencies
RUN apt-get install -y \
  python2.7 \
  python-dev \
  python-pip \
  build-essential \
  libyaml-dev

RUN pip install -r requirements.txt

WORKDIR /opt/TrackHubGenerator/
ENV PATH /opt/TrackHubGenerator:$PATH
CMD ["make"]<commit_msg>Include bedToBigBed in dockerfile<commit_after>FROM ubuntu:14.04
MAINTAINER <NAME> <<EMAIL>>

# fetchChromSizes can use mysql, wget, or FTP
RUN apt-get update && apt-get install -y \
  curl \
  wget \
  bedtools

WORKDIR /usr/local/bin

# Fetch tools from hgdownload and place in /usr/local/bin
RUN curl -SLO http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig
RUN curl -SLO http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed
RUN curl -SLO http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes
RUN curl -SLO http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/hubCheck
RUN curl -SLO http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver
RUN chmod +x *

# Add local code
RUN mkdir -p /opt/TrackHubGenerator
COPY . /opt/TrackHubGenerator
WORKDIR /opt/TrackHubGenerator/python

# Install python dependencies
RUN apt-get install -y \
  python2.7 \
  python-dev \
  python-pip \
  build-essential \
  libyaml-dev

RUN pip install -r requirements.txt

WORKDIR /opt/TrackHubGenerator/
ENV PATH /opt/TrackHubGenerator:$PATH
CMD ["make"]
{'fraction_non_alphanumeric': 0.11645813282001925, 'fraction_numerical': 0.023099133782483156, 'mean_word_length': 3.8013856812933025, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 9, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 11, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3243747', 'n_tokens_mistral': 823, 'n_tokens_neox': 765, 'n_words': 176}