<commit_before>FROM ubuntu:16.04

RUN apt-get clean all && apt-get update && apt-get install -y build-essential apt-utils git wget perl \
    python3.5 python3-pip debconf-utils sudo python-numpy cmake samtools bedtools zlib1g-dev libc6 aptitude \
    libdbd-mysql-perl libdbi-perl libboost-all-dev libncurses5-dev bowtie default-jre parallel nano bowtie2 exonerate

RUN rm /bin/sh && ln -s /bin/bash /bin/sh

RUN echo "mysql-server mysql-server/root_password password <PASSWORD>" | debconf-set-selections
RUN echo "mysql-server mysql-server/root_password_again password <PASSWORD>" | debconf-set-selections

RUN apt-get install -y mysql-server mysql-client mysql-common bowtie bioperl apache2 libcairo2-dev libpango1.0-dev 

RUN pip3 install biopython==1.68 bcbio-gff==0.6.4 pandas==0.19.1 pybedtools==0.7.8 gffutils regex pysam matplotlib

WORKDIR /opt/

RUN git clone git://github.com/pezmaster31/bamtools.git && cd bamtools && mkdir build && cd build &&\
    cmake .. && make && sudo make install && cd /usr/include &&  sudo ln -f -s ../local/include/bamtools/ &&\
    cd /usr/lib/ &&  sudo ln -f -s /usr/local/lib/bamtools/libbamtools.* .

RUN git clone https://github.com/lfaino/LoReAn.git && git clone https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library.git && \
mv Complete-Striped-Smith-Waterman-Library SW && cd SW/src/ && make && cp ssw_lib.py  /opt/LoReAn/code/ && cp libssw.so  /opt/LoReAn/code/

WORKDIR /opt/LoReAn/third_party/software/

RUN tar -zxvf AATpackage-r03052011.tgz && rm AATpackage-r03052011.tgz && cd AATpackage-r03052011 && make clean && sudo ./configure --prefix=$PWD && sudo make && sudo make install 

RUN tar -zxvf iAssembler-v1.3.2.x64.tgz && rm iAssembler-v1.3.2.x64.tgz && tar -zxvf gm_et_linux_64.tar.gz && rm gm_et_linux_64.tar.gz

RUN wget https://github.com/PASApipeline/PASApipeline/archive/v2.1.0.tar.gz && tar -zxvf v2.1.0.tar.gz && rm v2.1.0.tar.gz &&\
    mv PASApipeline-2.1.0 PASApipeline && cd PASApipeline && make clean && make && cd .. &&  cp ../conf_files/conf.txt PASApipeline/pasa_conf/
    
RUN wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.2.3.tar.gz && \
    tar -zxvf augustus-3.2.3.tar.gz && rm augustus-3.2.3.tar.gz && mv augustus-3.2.3 augustus && cd augustus  && make clean && make 
    
RUN wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.4.0.tar.gz && tar -zxvf Trinity-v2.4.0.tar.gz && mv trinityrnaseq-Trinity-v2.4.0 Trinity && \
    rm Trinity-v2.4.0.tar.gz && cd Trinity && make && make plugins 

RUN wget https://github.com/alexdobin/STAR/archive/2.5.2b.tar.gz && tar -xzf 2.5.2b.tar.gz && rm 2.5.2b.tar.gz &&\
    cd STAR-2.5.2b/source && make STAR && git submodule update --init --recursive 

RUN wget https://github.com/TransDecoder/TransDecoder/archive/v3.0.1.tar.gz &&  tar -zxvf v3.0.1.tar.gz && rm v3.0.1.tar.gz &&\
    cd TransDecoder-3.0.1 && make  

RUN wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2017-06-20.tar.gz && tar -zxvf gmap-gsnap-2017-06-20.tar.gz && rm gmap-gsnap-2017-06-20.tar.gz &&\
    mv gmap-2017-06-20/ gmap && cd gmap/  && ./configure && make && sudo make install

RUN wget http://faculty.virginia.edu/wrpearson/fasta/fasta36/fasta-36.3.8e.tar.gz && tar -zxvf fasta-36.3.8e.tar.gz && rm fasta-36.3.8e.tar.gz &&\
    cd fasta-36.3.8e/src && make -f ../make/Makefile.linux fasta36 && cp /opt/LoReAn/third_party/software/fasta-36.3.8e/bin/fasta36 /usr/local/bin/fasta

RUN wget http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1.tar.gz && tar -zxvf BRAKER1.tar.gz && rm BRAKER1.tar.gz && \
 wget https://github.com/EVidenceModeler/EVidenceModeler/archive/v1.1.1.tar.gz && tar -zxvf v1.1.1.tar.gz && rm v1.1.1.tar.gz


RUN wget https://downloads.sourceforge.net/project/splicegrapher/SpliceGrapher-0.2.5.tgz &&  tar -zxvf SpliceGrapher-0.2.5.tgz && \
    cd SpliceGrapher-0.2.5/ && python3 setup.py build && python3 setup.py install && cd .. \
    && git clone https://bitbucket.org/comp_bio/tapis.git && cd tapis && python3 setup.py build && python3 setup.py install

RUN sudo perl -MCPAN -e shell && sudo cpan -f -i YAML && sudo cpan -f -i Hash::Merge && sudo cpan -f -i  Logger::Simple && sudo cpan -f -i  Parallel::ForkManager &&\
    sudo cpan -f -i Config::Std && sudo cpan -f -i Scalar::Util::Numeric 
     
RUN mkdir gffread && cd gffread && git clone https://github.com/gpertea/gclib &&\
    git clone https://github.com/gpertea/gffread && cd gffread && make && cp ./gffread /usr/local/bin

RUN wget http://genometools.org/pub/genometools-1.5.9.tar.gz && \
     tar -zxvf genometools-1.5.9.tar.gz && rm genometools-1.5.9.tar.gz && cd genometools-1.5.9 && make

RUN cp ../conf_files/createUser.sh /usr/local/bin && cd /usr/local/bin && chmod -R 777 ./ && cd /opt/LoReAn/ && chmod -R 777 ./

RUN cp ../conf_files/pathToExport.txt /etc/profile.d/pathToExport.sh


WORKDIR /data/<commit_msg>new commit<commit_after>FROM ubuntu:16.04

RUN apt-get clean all && apt-get update && apt-get install -y build-essential apt-utils git wget perl \
    python3.5 python2.7 python3-pip python2.7-pip debconf-utils sudo python-numpy cmake samtools bedtools zlib1g-dev libc6 aptitude \
    libdbd-mysql-perl libdbi-perl libboost-all-dev libncurses5-dev bowtie default-jre parallel nano bowtie2 exonerate

RUN rm /bin/sh && ln -s /bin/bash /bin/sh

RUN echo "mysql-server mysql-server/root_password password <PASSWORD>" | debconf-set-selections
RUN echo "mysql-server mysql-server/root_password_again password <PASSWORD>" | debconf-set-selections

RUN apt-get install -y mysql-server mysql-client mysql-common bowtie bioperl apache2 libcairo2-dev libpango1.0-dev 

RUN pip3 install biopython==1.68 bcbio-gff==0.6.4 pandas==0.19.1 pybedtools==0.7.8 gffutils regex pysam matplotlib

RUN pip pysam matplotlib

WORKDIR /opt/

RUN git clone git://github.com/pezmaster31/bamtools.git && cd bamtools && mkdir build && cd build &&\
    cmake .. && make && sudo make install && cd /usr/include &&  sudo ln -f -s ../local/include/bamtools/ &&\
    cd /usr/lib/ &&  sudo ln -f -s /usr/local/lib/bamtools/libbamtools.* .

RUN git clone https://github.com/lfaino/LoReAn.git && git clone https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library.git && \
mv Complete-Striped-Smith-Waterman-Library SW && cd SW/src/ && make && cp ssw_lib.py  /opt/LoReAn/code/ && cp libssw.so  /opt/LoReAn/code/

WORKDIR /opt/LoReAn/third_party/software/

RUN tar -zxvf AATpackage-r03052011.tgz && rm AATpackage-r03052011.tgz && cd AATpackage-r03052011 && make clean && sudo ./configure --prefix=$PWD && sudo make && sudo make install 

RUN tar -zxvf iAssembler-v1.3.2.x64.tgz && rm iAssembler-v1.3.2.x64.tgz && tar -zxvf gm_et_linux_64.tar.gz && rm gm_et_linux_64.tar.gz

RUN wget https://github.com/PASApipeline/PASApipeline/archive/v2.1.0.tar.gz && tar -zxvf v2.1.0.tar.gz && rm v2.1.0.tar.gz &&\
    mv PASApipeline-2.1.0 PASApipeline && cd PASApipeline && make clean && make && cd .. &&  cp ../conf_files/conf.txt PASApipeline/pasa_conf/
    
RUN wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.2.3.tar.gz && \
    tar -zxvf augustus-3.2.3.tar.gz && rm augustus-3.2.3.tar.gz && mv augustus-3.2.3 augustus && cd augustus  && make clean && make 
    
RUN wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.4.0.tar.gz && tar -zxvf Trinity-v2.4.0.tar.gz && mv trinityrnaseq-Trinity-v2.4.0 Trinity && \
    rm Trinity-v2.4.0.tar.gz && cd Trinity && make && make plugins 

RUN wget https://github.com/alexdobin/STAR/archive/2.5.2b.tar.gz && tar -xzf 2.5.2b.tar.gz && rm 2.5.2b.tar.gz &&\
    cd STAR-2.5.2b/source && make STAR && git submodule update --init --recursive 

RUN wget https://github.com/TransDecoder/TransDecoder/archive/v3.0.1.tar.gz &&  tar -zxvf v3.0.1.tar.gz && rm v3.0.1.tar.gz &&\
    cd TransDecoder-3.0.1 && make  

RUN wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2017-06-20.tar.gz && tar -zxvf gmap-gsnap-2017-06-20.tar.gz && rm gmap-gsnap-2017-06-20.tar.gz &&\
    mv gmap-2017-06-20/ gmap && cd gmap/  && ./configure && make && sudo make install

RUN wget http://faculty.virginia.edu/wrpearson/fasta/fasta36/fasta-36.3.8e.tar.gz && tar -zxvf fasta-36.3.8e.tar.gz && rm fasta-36.3.8e.tar.gz &&\
    cd fasta-36.3.8e/src && make -f ../make/Makefile.linux fasta36 && cp /opt/LoReAn/third_party/software/fasta-36.3.8e/bin/fasta36 /usr/local/bin/fasta

RUN wget http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1.tar.gz && tar -zxvf BRAKER1.tar.gz && rm BRAKER1.tar.gz && \
 wget https://github.com/EVidenceModeler/EVidenceModeler/archive/v1.1.1.tar.gz && tar -zxvf v1.1.1.tar.gz && rm v1.1.1.tar.gz


RUN wget https://downloads.sourceforge.net/project/splicegrapher/SpliceGrapher-0.2.5.tgz &&  tar -zxvf SpliceGrapher-0.2.5.tgz && \
    cd SpliceGrapher-0.2.5/ && python setup.py build && python setup.py install && cd .. \
    && git clone https://bitbucket.org/comp_bio/tapis.git && cd tapis && python setup.py build && python setup.py install

RUN sudo perl -MCPAN -e shell && sudo cpan -f -i YAML && sudo cpan -f -i Hash::Merge && sudo cpan -f -i  Logger::Simple && sudo cpan -f -i  Parallel::ForkManager &&\
    sudo cpan -f -i Config::Std && sudo cpan -f -i Scalar::Util::Numeric 
     
RUN mkdir gffread && cd gffread && git clone https://github.com/gpertea/gclib &&\
    git clone https://github.com/gpertea/gffread && cd gffread && make && cp ./gffread /usr/local/bin

RUN wget http://genometools.org/pub/genometools-1.5.9.tar.gz && \
     tar -zxvf genometools-1.5.9.tar.gz && rm genometools-1.5.9.tar.gz && cd genometools-1.5.9 && make

RUN cp ../conf_files/createUser.sh /usr/local/bin && cd /usr/local/bin && chmod -R 777 ./ && cd /opt/LoReAn/ && chmod -R 777 ./

RUN cp ../conf_files/pathToExport.txt /etc/profile.d/pathToExport.sh


WORKDIR /data/
{'fraction_non_alphanumeric': 0.1632381537201924, 'fraction_numerical': 0.04707808822024358, 'mean_word_length': 3.1093355761143817, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 7, 'https://': 22, 'lorem ipsum': 0, 'www.': 0, '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': '2577865', 'n_tokens_mistral': 4199, 'n_tokens_neox': 3919, 'n_words': 810}