<commit_before>FROM ubuntu:20.04
MAINTAINER <NAME> (<EMAIL>)

#########
### Working dir
#########
RUN	mkdir build
WORKDIR /build

#########
### Setup the environment
#########
ENV DEBIAN_FRONTEND noninteractive
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en

#########
### Aptitude packages
#########
RUN apt update \
    && apt -y upgrade \
    && apt install -y --reinstall language-pack-en \
    && locale-gen en_US.UTF-8
RUN apt update && apt install -y build-essential git cmake python3 python3-pip autoconf libbz2-dev liblzma-dev libxml2-dev libz-dev curl wget sudo nano


#########
### Python modules
#########
RUN pip3 install --upgrade pip

#########
### Create user orp
#########
RUN useradd -r -s /bin/bash -U -m -d /home/orp -p '' orp

#########
### Setup the user environment
########
ENV HOME /home/orp
RUN usermod -aG sudo,audio,video orp \
&& echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers

#########
### Oyster River Protocol (ORP)
#########
WORKDIR /home/orp
USER orp
RUN git clone https://github.com/macmanes-lab/Oyster_River_Protocol.git
RUN cd Oyster_River_Protocol && sudo make
RUN sed -i  "s_ubuntu_orp_g" /home/orp/Oyster_River_Protocol/software/config.ini

#########
### Path
#########
RUN echo 'PATH=$PATH:/home/orp/Oyster_River_Protocol/software/anaconda/install/bin' >> /home/orp/.profile
RUN echo 'PATH=$PATH:/home/orp/Oyster_River_Protocol/software/OrthoFinder/orthofinder' >> /home/orp/.profile
RUN echo 'export TRINITY_HOME=/home/orp/Oyster_River_Protocol/software/trinityrnaseq-v2.12.0/ >> /home/orp/.profile
RUN echo 'PATH=$PATH:/home/orp/Oyster_River_Protocol/software/SPAdes-3.15.2-Linux/bin/' >> /home/orp/.profile
RUN echo 'PATH=$PATH:/home/orp/Oyster_River_Protocol/software/orp-transrate' >> /home/orp/.profile
RUN echo 'PATH=$PATH:/home/orp/Oyster_River_Protocol/software/transabyss' >> /home/orp/.profile
RUN /bin/bash -c "source /home/orp/.profile"
ENV PATH="/home/orp/Oyster_River_Protocol/software/transabyss:/home/orp/Oyster_River_Protocol/software/orp-transrate:/home/orp/Oyster_River_Protocol/software/OrthoFinder/orthofinder:/home/orp/Oyster_River_Protocol/software/anaconda/install/bin:${PATH}"

#########
### Clean up
#########
USER root
WORKDIR /
RUN rm -rf /build

#########
### Setup init workspace
#########
WORKDIR $HOME
USER orp
RUN /bin/bash -c "source activate orp"<commit_msg>unquoted string fix<commit_after>FROM ubuntu:20.04
MAINTAINER <NAME> (<EMAIL>)

#########
### Working dir
#########
RUN	mkdir build
WORKDIR /build

#########
### Setup the environment
#########
ENV DEBIAN_FRONTEND noninteractive
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en

#########
### Aptitude packages
#########
RUN apt update \
    && apt -y upgrade \
    && apt install -y --reinstall language-pack-en \
    && locale-gen en_US.UTF-8
RUN apt update && apt install -y build-essential git cmake python3 python3-pip autoconf libbz2-dev liblzma-dev libxml2-dev libz-dev curl wget sudo nano


#########
### Python modules
#########
RUN pip3 install --upgrade pip

#########
### Create user orp
#########
RUN useradd -r -s /bin/bash -U -m -d /home/orp -p '' orp

#########
### Setup the user environment
########
ENV HOME /home/orp
RUN usermod -aG sudo,audio,video orp \
&& echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers

#########
### Oyster River Protocol (ORP)
#########
WORKDIR /home/orp
USER orp
RUN git clone https://github.com/macmanes-lab/Oyster_River_Protocol.git
RUN cd Oyster_River_Protocol && sudo make
RUN sed -i  "s_ubuntu_orp_g" /home/orp/Oyster_River_Protocol/software/config.ini

#########
### Path
#########
RUN echo 'PATH=$PATH:/home/orp/Oyster_River_Protocol/software/anaconda/install/bin' >> /home/orp/.profile
RUN echo 'PATH=$PATH:/home/orp/Oyster_River_Protocol/software/OrthoFinder/orthofinder' >> /home/orp/.profile
RUN echo 'export TRINITY_HOME=/home/orp/Oyster_River_Protocol/software/trinityrnaseq-v2.12.0/' >> /home/orp/.profile
RUN echo 'PATH=$PATH:/home/orp/Oyster_River_Protocol/software/SPAdes-3.15.2-Linux/bin/' >> /home/orp/.profile
RUN echo 'PATH=$PATH:/home/orp/Oyster_River_Protocol/software/orp-transrate' >> /home/orp/.profile
RUN echo 'PATH=$PATH:/home/orp/Oyster_River_Protocol/software/transabyss' >> /home/orp/.profile
RUN /bin/bash -c "source /home/orp/.profile"
ENV PATH="/home/orp/Oyster_River_Protocol/software/transabyss:/home/orp/Oyster_River_Protocol/software/orp-transrate:/home/orp/Oyster_River_Protocol/software/OrthoFinder/orthofinder:/home/orp/Oyster_River_Protocol/software/anaconda/install/bin:${PATH}"

#########
### Clean up
#########
USER root
WORKDIR /
RUN rm -rf /build

#########
### Setup init workspace
#########
WORKDIR $HOME
USER orp
RUN /bin/bash -c "source activate orp"
{'fraction_non_alphanumeric': 0.19822297440236936, 'fraction_numerical': 0.008462026655383965, 'mean_word_length': 4.703256936067551, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 35, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, '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': '3908907', 'n_tokens_mistral': 1759, 'n_tokens_neox': 1666, 'n_words': 355}