<commit_before># Copyright (c) Bioinformatics Core Facility of the Max Planck Institute for Biology of Ageing.
# Distributed under the terms of the Modified BSD License.

FROM mpgagebioinformatics/bioinformatics_software:v4.0.0-1

LABEL maintainer "<EMAIL>"

USER root

#########################################
#### Bioinformatics tools start here ####
#########################################

# Installing QUAST
RUN /bin/bash -c 'source /etc/profile.d/modules.sh && \
  module load python/3.9.13 && \
  module load perl && \
  mkdir -p $SOFT/quast/5.2.0/bin && \
  export PYTHONUSERBASE=$SOFT/quast/5.2.0/ && \
  pip3 install future --user && \
  pip3 install qutils --user && \
  pip3 install matplotlib --user && \
  cpanm Time::HiRes -l $SOFT/quast/5.2.0/ && \
  export PERL5LIB=$SOFT/quast/5.2.0/lib/perl5:$PERL5LIB && \
  cd $SOUR && \
  wget https://downloads.sourceforge.net/project/quast/quast-5.2.0.tar.gz && \
  tar -xzf quast-5.2.0.tar.gz && \
  cd quast-5.2.0 && \
  python3 setup.py install --user && \
  cp -r * $SOFT/quast/5.2.0/bin/ && \
  newmod.sh \
  -s quast \
  -p $MODF/bioinformatics/ \
  -v 5.2.0 \
  -d 5.2.0 && \
  echo "module load perl python/3.9.13" && \
  echo "setenv PYTHONUSERBASE $SOFT/quast/5.2.0/lib/python3.8" >> $MODF/bioinformatics/quast/5.2.0 && \
  echo "prepend-path PERL5LIB $SOFT/quast/5.2.0/lib/perl5" >> $MODF/bioinformatics/quast/5.2.0 && \
  echo "module load perl python" >> $MODF/bioinformatics/quast/5.2.0' && \
  rm -rf ${SOUR}/*

# Installing BLAST+
RUN mkdir -p $SOFT/blast/2.13.0 && \
  cd $SOUR && \
  wget -O d.tar.gz ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.13.0+-x64-linux.tar.gz && \
  mv d.tar.gz ncbi-blast-2.13.0+-x64-linux.tar.gz && \
  tar -xzf ncbi-blast-2.13.0+-x64-linux.tar.gz && \
  cd ncbi-blast-2.13.0+ && \
  cp -r * $SOFT/blast/2.13.0 && \
  chmod 775 $SOFT/blast/2.13.0/bin/* && \
  newmod.sh \
  -s blast \
  -p $MODF/bioinformatics/ \
  -v 2.13.0 \
  -d 2.13.0 && \
  rm -rf ${SOUR}/*

# Installing primer3 
RUN mkdir -p $SOFT/primer3/2.6.1/bin && \
  cd $SOUR && \
  wget https://github.com/primer3-org/primer3/archive/v2.6.1.tar.gz && \
  tar -xzf v2.6.1.tar.gz && \
  cd primer3-2.6.1/src && \
  make all && \
  cp -r * $SOFT/primer3/2.6.1/bin && \
  newmod.sh \
  -s primer3 \
  -p $MODF/bioinformatics/ \
  -v 2.6.1 \
  -d 2.6.1 && \
  rm -rf ${SOUR}/*

# Installing trimmomatic
RUN /bin/bash -c 'source /etc/profile.d/modules.sh && \
  mkdir -p $SOFT/trimmomatic/0.39/bin && \
  module load jdk && \
  cd $SOUR && \ 
  wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip && \
  unzip Trimmomatic-0.39.zip && \
  cd Trimmomatic-0.39 && \
  cp -r * $SOFT/trimmomatic/0.39/bin && \
  chmod 775 $SOFT/trimmomatic/0.39/bin/*.jar && \
  newmod.sh \
  -s trimmomatic \
  -p $MODF/bioinformatics/ \
  -v 0.39 \
  -d 0.39 && \
  echo "module load jdk" >> $MODF/bioinformatics/trimmomatic/0.39 && \
  echo "setenv TRIMMOMATIC $SOFT/trimmomatic/0.39/bin/trimmomatic-0.39.jar" >> $MODF/bioinformatics/trimmomatic/0.39' && \
  rm -rf ${SOUR}/*

# methpipe
RUN /bin/bash -c 'source /etc/profile.d/modules.sh && \
  module load gsl && \
  cd $SOUR && wget http://smithlabresearch.org/downloads/methpipe-5.0.0.tar.gz && \
  wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.tar.bz2 && \
  mkdir -p $SOFT/methpipe/5.0.0 && \
  tar -zxvf methpipe-5.0.0.tar.gz && \
  tar -jxvf htslib-1.16.tar.bz2 && \
  cd htslib-1.16 && \
  ./configure --prefix=$SOFT/methpipe/5.0.0 && make && make install && \
  cd $SOUR/methpipe-5.0.0 && \
  mkdir build && cd build && \
  ../configure --prefix=$SOFT/methpipe/5.0.0 CPPFLAGS='-I $SOFT/methpipe/5.0.0/include/htslib' LDFLAGS='-L$SOFT/methpipe/5.0.0/lib' && \
  make && \
  make install && \
  cp -r *  $SOFT/methpipe/5.0.0/ && \
  newmod.sh \
  -s methpipe \
  -p $MODF/bioinformatics/ \
  -v 5.0.0 \
  -d 5.0.0 && \
  echo "module load gsl" >> $MODF/bioinformatics/methpipe/5.0.0' && \
  rm -rf ${SOUR}/*

# walt
RUN /bin/bash -c 'source /etc/profile.d/modules.sh && \
  module load gsl && \
  cd $SOUR && wget https://github.com/smithlabcode/walt/archive/v1.01.tar.gz && \
  tar -zxvf v1.01.tar.gz && \
  mkdir -p $SOFT/walt/1.1.0 && \
  cd walt-1.01 && \
  make all && \
  make install && \
  cp -r * $SOFT/walt/1.1.0/ && \
  newmod.sh \<commit_msg>New from ground up<commit_after># Copyright (c) Bioinformatics Core Facility of the Max Planck Institute for Biology of Ageing.
# Distributed under the terms of the Modified BSD License.

FROM mpgagebioinformatics/bioinformatics_software:v4.0.0-1

LABEL maintainer "<EMAIL>"

USER root

#########################################
#### Bioinformatics tools start here ####
#########################################

# Installing QUAST
RUN /bin/bash -c 'source /etc/profile.d/modules.sh && \
  module load python/3.9.13 && \
  module load perl && \
  mkdir -p $SOFT/quast/5.2.0/bin && \
  export PYTHONUSERBASE=$SOFT/quast/5.2.0/ && \
  pip3 install future --user && \
  pip3 install qutils --user && \
  pip3 install matplotlib --user && \
  cpanm Time::HiRes -l $SOFT/quast/5.2.0/ && \
  export PERL5LIB=$SOFT/quast/5.2.0/lib/perl5:$PERL5LIB && \
  cd $SOUR && \
  wget https://downloads.sourceforge.net/project/quast/quast-5.2.0.tar.gz && \
  tar -xzf quast-5.2.0.tar.gz && \
  cd quast-5.2.0 && \
  python3 setup.py install --user && \
  cp -r * $SOFT/quast/5.2.0/bin/ && \
  newmod.sh \
  -s quast \
  -p $MODF/bioinformatics/ \
  -v 5.2.0 \
  -d 5.2.0 && \
  echo "module load perl python/3.9.13" && \
  echo "setenv PYTHONUSERBASE $SOFT/quast/5.2.0/lib/python3.8" >> $MODF/bioinformatics/quast/5.2.0 && \
  echo "prepend-path PERL5LIB $SOFT/quast/5.2.0/lib/perl5" >> $MODF/bioinformatics/quast/5.2.0 && \
  echo "module load perl python" >> $MODF/bioinformatics/quast/5.2.0' && \
  rm -rf ${SOUR}/*

# Installing BLAST+
RUN mkdir -p $SOFT/blast/2.13.0 && \
  cd $SOUR && \
  wget -O d.tar.gz ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.13.0+-x64-linux.tar.gz && \
  mv d.tar.gz ncbi-blast-2.13.0+-x64-linux.tar.gz && \
  tar -xzf ncbi-blast-2.13.0+-x64-linux.tar.gz && \
  cd ncbi-blast-2.13.0+ && \
  cp -r * $SOFT/blast/2.13.0 && \
  chmod 775 $SOFT/blast/2.13.0/bin/* && \
  newmod.sh \
  -s blast \
  -p $MODF/bioinformatics/ \
  -v 2.13.0 \
  -d 2.13.0 && \
  rm -rf ${SOUR}/*

# Installing primer3 
RUN mkdir -p $SOFT/primer3/2.6.1/bin && \
  cd $SOUR && \
  wget https://github.com/primer3-org/primer3/archive/v2.6.1.tar.gz && \
  tar -xzf v2.6.1.tar.gz && \
  cd primer3-2.6.1/src && \
  make all && \
  cp -r * $SOFT/primer3/2.6.1/bin && \
  newmod.sh \
  -s primer3 \
  -p $MODF/bioinformatics/ \
  -v 2.6.1 \
  -d 2.6.1 && \
  rm -rf ${SOUR}/*

# Installing trimmomatic
RUN /bin/bash -c 'source /etc/profile.d/modules.sh && \
  mkdir -p $SOFT/trimmomatic/0.39/bin && \
  module load jdk && \
  cd $SOUR && \ 
  wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip && \
  unzip Trimmomatic-0.39.zip && \
  cd Trimmomatic-0.39 && \
  cp -r * $SOFT/trimmomatic/0.39/bin && \
  chmod 775 $SOFT/trimmomatic/0.39/bin/*.jar && \
  newmod.sh \
  -s trimmomatic \
  -p $MODF/bioinformatics/ \
  -v 0.39 \
  -d 0.39 && \
  echo "module load jdk" >> $MODF/bioinformatics/trimmomatic/0.39 && \
  echo "setenv TRIMMOMATIC $SOFT/trimmomatic/0.39/bin/trimmomatic-0.39.jar" >> $MODF/bioinformatics/trimmomatic/0.39' && \
  rm -rf ${SOUR}/*

# methpipe
RUN /bin/bash -c 'source /etc/profile.d/modules.sh && \
  module load gsl && \
  cd $SOUR && wget http://smithlabresearch.org/downloads/methpipe-5.0.0.tar.gz && \
  wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.tar.bz2 && \
  mkdir -p $SOFT/methpipe/5.0.0 && \
  tar -zxvf methpipe-5.0.0.tar.gz && \
  tar -jxvf htslib-1.16.tar.bz2 && \
  cd htslib-1.16 && \
  ./configure --prefix=$SOFT/methpipe/5.0.0 && make && make install && \
  cd $SOUR/methpipe-5.0.0 && \
  mkdir build && cd build && \
  ../configure --prefix=$SOFT/methpipe/5.0.0 CPPFLAGS='-I /modules/software/methpipe/5.0.0/include' LDFLAGS='-L/modules/software/methpipe/5.0.0/lib' && \
  make && \
  make install && \
  cp -r ../*  $SOFT/methpipe/5.0.0/ && \
  newmod.sh \
  -s methpipe \
  -p $MODF/bioinformatics/ \
  -v 5.0.0 \
  -d 5.0.0 && \
  echo "module load gsl" >> $MODF/bioinformatics/methpipe/5.0.0' && \
  rm -rf ${SOUR}/*

# abismal
RUN /bin/bash -c 'source /etc/profile.d/modules.sh && \
  cd $SOUR && wget https://github.com/smithlabcode/abismal/releases/download/v3.0.0/abismal-3.0.0.tar.gz && \
  tar -zxvf abismal-3.0.0.tar.gz && \
  mkdir -p $SOFT/abismal/3.0.0 && \
  cd abismal-3.0.0 && \
  ./configure --prefix=$SOFT/abismal/3.0.0 && \
  make all && \
  make install && \
  newmod.sh \
  -s abismal \
  -p $MODF/bioinformatics/ \
  -v 3.0.0 \
  -d 3.0.0 && \
  rm -rf ${SOUR}/*

# walt
RUN /bin/bash -c 'source /etc/profile.d/modules.sh && \
  module load gsl && \
  cd $SOUR && wget https://github.com/smithlabcode/walt/archive/v1.01.tar.gz && \
  tar -zxvf v1.01.tar.gz && \
  mkdir -p $SOFT/walt/1.1.0 && \
  cd walt-1.01 && \
  make all && \
  make install && \
  cp -r * $SOFT/walt/1.1.0/ && \
  newmod.sh \
{'fraction_non_alphanumeric': 0.21856613641316192, 'fraction_numerical': 0.05600348659838745, 'mean_word_length': 2.3438979963570126, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 29, 'https://': 9, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 7, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5256619', 'n_tokens_mistral': 4367, 'n_tokens_neox': 4067, 'n_words': 705}