<commit_before>FROM ubuntu:14.04

MAINTAINER <NAME> <<EMAIL>>

RUN apt-get update && apt-get install -qqy build-essential

ADD http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.1.tar.gz /opt/
RUN cd /opt && \
    tar -xzvf augustus* && \
    rm -rf *.tar.gz && \
    mv augustus* augustus && \
    cd augustus && \
    make

ADD fgram_base /opt/augustus/config/species/    
ENV AUGUSTUS_CONFIG_PATH /opt/augustus/config
ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/augustus/bin:/opt/augustus/scripts
CMD ["/opt/augustus/bin/augustus"]<commit_msg>Update to latest version of Augustus (3.3)<commit_after>FROM ubuntu:16.04

MAINTAINER <NAME> <<EMAIL>>

RUN apt-get update \
&& apt-get install -qqy \
build-essential \
libbamtools-dev \
libboost-graph-dev \
libboost-iostreams-dev \
libgsl-dev \
liblpsolve55-dev \
libsqlite3-dev \
libsuitesparse-dev \
wget \
zlib1g-dev

WORKDIR /usr/local

# Install Augustus
RUN wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus.current.tar.gz \
&& tar -xvf augustus*.tar.gz \
&& rm augustus*.tar.gz \
&& cd augustus \
&& echo "COMPGENEPRED = true" >> common.mk \
&& make \
&& make install

ENV AUGUSTUS_CONFIG_PATH /usr/local/augustus/config
ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/augustus/bin:/usr/local/augustus/scripts
{'fraction_non_alphanumeric': 0.15840118430792005, 'fraction_numerical': 0.011843079200592153, 'mean_word_length': 3.506666666666667, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 11, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, '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': '7533707', 'n_tokens_mistral': 567, 'n_tokens_neox': 537, 'n_words': 94}