<commit_before>############################################################
# Dockerfile to build MATAM container images
# Based on Debian
############################################################

# Set the base image to Debian
FROM debian

# File Author / Maintainer
MAINTAINER <NAME>

################## BEGIN INSTALLATION ######################
# Install MATAM following the instructions from Github repository
# Ref: https://github.com/bonsai-team/matam

# Install dependencies
RUN apt-get update && apt-get install --no-install-recommends -y \
    git \
    gcc \
    g++ \
    wget \
    bash \
    default-jdk \
    automake \
    make \
    cmake \
    libsparsehash-dev \
    zlib1g-dev \
    bzip2
    # Python 3 now comes from conda

# Install Conda
RUN wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
    && bash Miniconda3-latest-Linux-x86_64.sh -b
ENV PATH /root/miniconda3/bin:$PATH

# Install Bioconda and samtools
RUN conda config --add channels conda-forge \
    && conda config --add channels defaults \
    && conda config --add channels r \
    && conda config --add channels bioconda
RUN conda install --update-dependencies -y samtools

# Clean apt cache
RUN rm -rf /var/lib/apt/lists/*
<commit_msg>Update the Dockerfile to fix the missing dependencie #20<commit_after>############################################################
# Dockerfile to build MATAM container images
# Based on Debian
############################################################

# Set the base image to Debian
FROM debian

# File Author / Maintainer
MAINTAINER <NAME>

################## BEGIN INSTALLATION ######################
# Install MATAM following the instructions from Github repository
# Ref: https://github.com/bonsai-team/matam

# Install dependencies
RUN apt-get update && apt-get install --no-install-recommends -y \
    git \
    gcc \
    g++ \
    wget \
    bash \
    default-jdk \
    automake \
    make \
    cmake \
    libsparsehash-dev \
    zlib1g-dev \
    bzip2 \
    ant
    # Python 3 now comes from conda

# Install Conda
RUN wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
    && bash Miniconda3-latest-Linux-x86_64.sh -b
ENV PATH /root/miniconda3/bin:$PATH

# Install Bioconda and samtools
RUN conda config --add channels conda-forge \
    && conda config --add channels defaults \
    && conda config --add channels r \
    && conda config --add channels bioconda
RUN conda install --update-dependencies -y samtools

# Clean apt cache
RUN rm -rf /var/lib/apt/lists/*

{'fraction_non_alphanumeric': 0.20695040999609526, 'fraction_numerical': 0.011714174150722375, 'mean_word_length': 3.27, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 4, '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': '2577845', 'n_tokens_mistral': 807, 'n_tokens_neox': 758, 'n_words': 231}