<commit_before>############################################################
# Dockerfile to build 16S rRNA diversity analysis
# Based on Ubuntu 16.04
############################################################

# Set the base image to Ubuntu
FROM ubuntu:16.04

# File Author / Maintainer
MAINTAINER <NAME> "<EMAIL>"

# Update the repository sources list
RUN apt-get update
RUN apt-get upgrade -y

WORKDIR /root

################## BEGIN INSTALLATION ######################
# Install Basic tools
RUN apt-get install -y wget unzip bzip2 sudo libfile-util-perl

# Install USEARCH
# Ref: http://www.drive5.com/usearch/manual/install.html
#ADD usearch8.1.1861_i86linux32 /usr/local/bin/
COPY usearch8.1.1861_i86linux32 /usr/local/bin/
RUN chmod +x /usr/local/bin/usearch8.1.1861_i86linux32
RUN ln -s /usr/local/bin/usearch8.1.1861_i86linux32 /usr/local/bin/usearch8

RUN wget http://kirill-kryukov.com/study/tools/fasta-splitter/files/fasta-splitter-0.2.4.zip
RUN unzip fasta-splitter-0.2.4.zip
RUN chmod +x fasta-splitter.pl
RUN mv fasta-splitter.pl /usr/local/bin/

# Based on https://hub.docker.com/r/continuumio/miniconda/~/dockerfile/
RUN echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
    wget --quiet https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
    rm ~/miniconda.sh
ENV PATH /opt/conda/bin:$PATH

# Install scripts
RUN wget http://drive5.com/python/python_scripts.tar.gz \
    && tar zxvf python_scripts.tar.gz -C /usr/local/bin/

RUN wget https://raw.githubusercontent.com/h3abionet/h3abionet16S/master/helpers/uparse_global_search_workaround.sh
RUN chmod +x uparse_global_search_workaround.sh
RUN mv uparse_global_search_workaround.sh /usr/local/bin/
##################### INSTALLATION END #####################

#ENTRYPOINT ["/usr/local/bin/usearch8.1.1861_i86linux32"]
#ENTRYPOINT ["/usr/local/bin/usearch8"]<commit_msg>Added some info on how to request to get access to the usearch binary, how to dowload it and where it needs to be placed so that it can picked up during the docker setup. Keeping the naming to usearch and not to a specific version. Version 9 is already available.<commit_after>############################################################
# Dockerfile to build 16S rRNA diversity analysis
# Based on Ubuntu 16.04
############################################################

# Set the base image to Ubuntu
FROM ubuntu:16.04

# File Author / Maintainer
MAINTAINER <NAME> "<EMAIL>"

# Update the repository sources list
RUN apt-get update
RUN apt-get upgrade -y

WORKDIR /root

################## BEGIN INSTALLATION ######################
# Install Basic tools
RUN apt-get install -y wget unzip bzip2 sudo libfile-util-perl

# Install USEARCH
# Follow instructions to get usearch here: http://www.drive5.com/usearch/download.html and then download from the link send by an email to the directory in which this Docker file resides. This is important! 
# E.g. cd /directory_where_this_docker_file_is; wget http://link_in_email -O usearch
COPY usearch /usr/local/bin/
RUN chmod +x /usr/local/bin/usearch

RUN wget http://kirill-kryukov.com/study/tools/fasta-splitter/files/fasta-splitter-0.2.4.zip
RUN unzip fasta-splitter-0.2.4.zip
RUN chmod +x fasta-splitter.pl
RUN mv fasta-splitter.pl /usr/local/bin/

# Based on https://hub.docker.com/r/continuumio/miniconda/~/dockerfile/
RUN echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
    wget --quiet https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
    rm ~/miniconda.sh
ENV PATH /opt/conda/bin:$PATH

# Install scripts
RUN wget http://drive5.com/python/python_scripts.tar.gz \
    && tar zxvf python_scripts.tar.gz -C /usr/local/bin/

RUN wget https://raw.githubusercontent.com/h3abionet/h3abionet16S/master/helpers/uparse_global_search_workaround.sh
RUN chmod +x uparse_global_search_workaround.sh
RUN mv uparse_global_search_workaround.sh /usr/local/bin/
##################### INSTALLATION END #####################
{'fraction_non_alphanumeric': 0.20101719544683944, 'fraction_numerical': 0.026398643739404214, 'mean_word_length': 4.434210526315789, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 9, 'https://': 6, 'lorem ipsum': 0, 'www.': 2, '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': '5424680', 'n_tokens_mistral': 1499, 'n_tokens_neox': 1395, 'n_words': 345}