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Optimised Dockerfile based on Best practices (ref: #19) #20

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249 changes: 104 additions & 145 deletions Dockerfile
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FROM ubuntu:xenial

RUN apt-get clean all && apt-get update && apt-get install -y -q build-essential git wget perl \
WORKDIR /opt/

RUN apt-get clean all && apt-get update && apt-get install -y -q --fix-missing build-essential git wget perl \
python3.5 python2.7 software-properties-common python3-pip python-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 \
bzip2 liblzma-dev libbz2-dev software-properties-common libboost-iostreams-dev libboost-system-dev libboost-filesystem-dev \
zlibc gcc-multilib apt-utils zlib1g-dev cmake tcsh g++ iputils-ping jellyfish bowtie bioperl apache2 libcairo2-dev libpango1.0-dev

RUN echo "mysql-server mysql-server/root_password password lorean" | debconf-set-selections

RUN echo "mysql-server mysql-server/root_password_again password lorean" | debconf-set-selections

RUN apt-get install -y mysql-server mysql-client mysql-common

RUN pip3 install numpy biopython==1.68 bcbio-gff==0.6.4 pandas==0.19.1 pybedtools==0.7.8 gffutils regex pysam matplotlib progressbar2 \
psutil memory_profiler pathlib colorama simplesam tqdm Flask

WORKDIR /opt/

RUN git clone https://github.com/lfaino/LoReAn.git

WORKDIR /opt/LoReAn/third_party/software/

RUN tar -zxvf Porechop.tar.gz && cd Porechop && make clean && make && cp porechop/cpp_functions.so /opt/LoReAn/code/

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 tar -zxvf SE-MEI.tar.gz && cd SE-MEI && make
zlibc gcc-multilib apt-utils zlib1g-dev cmake tcsh g++ iputils-ping jellyfish bowtie bioperl apache2 libcairo2-dev libpango1.0-dev \
bamtools libbamtools-dev liblzma-dev automake autoconf \
libcurl4-gnutls-dev libssl-dev \
hmmer locales && \
locale-gen en_US.UTF-8 && update-locale && \
echo "mysql-server mysql-server/root_password password lorean" | debconf-set-selections && \
echo "mysql-server mysql-server/root_password_again password lorean" | debconf-set-selections && \
apt-get install -y mysql-server mysql-client mysql-common && \
pip3 install numpy biopython==1.68 bcbio-gff==0.6.4 pandas==0.19.1 pybedtools==0.7.8 gffutils regex pysam matplotlib progressbar2 \
psutil memory_profiler pathlib colorama simplesam tqdm Flask && \
chmod a+w /opt/ && \
git clone https://github.com/lfaino/LoReAn.git

WORKDIR /opt/LoReAn/third_party/software

COPY PASApipeline-v2.3.3.tar.gz ./

RUN tar -zxvf PASApipeline-v2.3.3.tar.gz && rm PASApipeline-v2.3.3.tar.gz &&\
mv PASApipeline-v2.3.3 PASApipeline && cd PASApipeline && make clean && make && cd .. && cp ../conf_files/conf.txt PASApipeline/pasa_conf/ &&\
cp ../scripts/process_GMAP_alignments_gff3_chimeras_ok.pl PASApipeline/scripts/ && chmod 775 PASApipeline/scripts/process_GMAP_alignments_gff3_chimeras_ok.pl

RUN apt-get install -y -q bamtools libbamtools-dev liblzma-dev automake autoconf

RUN git clone https://github.com/samtools/htslib.git && cd htslib && autoheader && autoconf && ./configure && make &&\
sudo make install && cd .. && git clone https://github.com/samtools/bcftools.git && cd bcftools && autoheader &&\
autoconf && ./configure && make && sudo make install && cd .. && git clone https://github.com/samtools/tabix.git &&\
cd tabix && make && cd .. && git clone https://github.com/samtools/samtools.git && cd samtools && autoheader &&\
autoconf -Wno-syntax && ./configure && make && sudo make install

RUN apt-get update && apt-get install -y -q --fix-missing libcurl4-gnutls-dev libssl-dev

RUN export TOOLDIR=/opt/LoReAn/third_party/software && git clone https://github.com/Gaius-Augustus/Augustus.git &&\
mv Augustus augustus && cd augustus && make clean && make

COPY Trinity-v2.5.1.tar.gz ./

RUN tar -zxvf Trinity-v2.5.1.tar.gz && \
mv trinityrnaseq-Trinity-v2.5.1 Trinity &&rm Trinity-v2.5.1.tar.gz && cd Trinity && make && make plugins

RUN git clone https://github.com/lh3/minimap2.git && cd minimap2 && make

RUN git clone https://github.com/alexdobin/STAR.git

COPY v3.0.1.tar.gz ./

RUN tar -zxvf v3.0.1.tar.gz && rm v3.0.1.tar.gz &&\
cd TransDecoder-3.0.1 && make

COPY gmap-gsnap-2017-11-15.tar.gz ./

RUN tar -zxvf gmap-gsnap-2017-11-15.tar.gz && rm gmap-gsnap-2017-11-15.tar.gz && \
mv gmap-2017-11-15 gmap && cd gmap/ && ./configure && make && sudo make install

COPY fasta-36.3.8e.tar.gz ./

RUN 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 git clone https://github.com/Gaius-Augustus/BRAKER.git

COPY v1.1.1.tar.gz ./

RUN tar -zxvf v1.1.1.tar.gz && rm v1.1.1.tar.gz

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 && sudo cpan -f -i File::Which

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

COPY genometools-1.5.9.tar.gz ./

RUN tar -zxvf genometools-1.5.9.tar.gz && rm genometools-1.5.9.tar.gz && cd genometools-1.5.9 && make

RUN cp ../../code/createUser.py /usr/local/bin && chmod 775 /usr/local/bin/createUser.py

RUN rm /opt/LoReAn/third_party/software/EVidenceModeler-1.1.1/EvmUtils/misc/cufflinks_gtf_to_alignment_gff3.pl

RUN sudo chmod -R 775 /opt/LoReAn/code/

COPY interproscan-5.27-66.0-64-bit.tar.gz ./

RUN tar -pxvzf interproscan-5.27-66.0-64-bit.tar.gz && rm interproscan-5.27-66.0-64-bit.tar.gz

WORKDIR /opt/LoReAn/third_party/software/interproscan-5.27-66.0

RUN mkdir cddblast

COPY ncbi-blast-2.7.1+-x64-linux.tar.gz ./cddblast

RUN cd cddblast && tar -zxvf ncbi-blast-2.7.1+-x64-linux.tar.gz && cp -r ncbi-blast-2.7.1+ ../bin/blast

COPY ncbi-blast-2.7.1+-x64-linux.tar.gz ./
COPY signalp-4.1f.Linux.tar.gz ./

RUN tar -xzf signalp-4.1f.Linux.tar.gz -C bin/signalp/4.1 --strip-components 1 && rm signalp-4.1f.Linux.tar.gz

COPY signalp-4.1/signalp bin/signalp/4.1/

RUN mkdir /data_panther

COPY tmhmm-2.0c.Linux.tar.gz ./

RUN tar -xzf tmhmm-2.0c.Linux.tar.gz -C ./ && cp tmhmm-2.0c/bin/decodeanhmm.Linux_x86_64 bin/tmhmm/2.0c/decodeanhmm && \
cp tmhmm-2.0c/lib/TMHMM2.0.model data/tmhmm/2.0c/TMHMM2.0c.model

RUN cp /opt/LoReAn/third_party/conf_files/interproscan.properties ./interproscan.properties

WORKDIR /usr/local/bin

RUN apt-get install -y -q hmmer

COPY trf ./
COPY trf /usr/local/bin
COPY RepeatScout-1.0.5.tar.gz /usr/local
COPY RepeatMasker-open-4-0-7.tar.gz /usr/local

RUN tar -zxvf Porechop.tar.gz && cd Porechop && make clean && make && cp porechop/cpp_functions.so /opt/LoReAn/code/ && \
cd /opt/LoReAn/third_party/software && \
tar -zxvf AATpackage-r03052011.tgz && rm AATpackage-r03052011.tgz && cd AATpackage-r03052011 && make clean && \
sudo ./configure --prefix=$PWD && sudo make && sudo make install && \
cd /opt/LoReAn/third_party/software && \
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 && \
tar -zxvf SE-MEI.tar.gz && cd SE-MEI && make && \
cd /opt/LoReAn/third_party/software && \
tar -zxvf PASApipeline-v2.3.3.tar.gz && rm PASApipeline-v2.3.3.tar.gz &&\
mv PASApipeline-v2.3.3 PASApipeline && cd PASApipeline && make clean && make && cd .. && cp ../conf_files/conf.txt PASApipeline/pasa_conf/ &&\
cp ../scripts/process_GMAP_alignments_gff3_chimeras_ok.pl PASApipeline/scripts/ && chmod 775 PASApipeline/scripts/process_GMAP_alignments_gff3_chimeras_ok.pl && \
cd /opt/LoReAn/third_party/software && \
git clone https://github.com/samtools/htslib.git && cd htslib && autoheader && autoconf && ./configure && make &&\
sudo make install && cd .. && git clone https://github.com/samtools/bcftools.git && cd bcftools && autoheader &&\
autoconf && ./configure && make && sudo make install && cd .. && git clone https://github.com/samtools/tabix.git &&\
cd tabix && make && cd .. && git clone https://github.com/samtools/samtools.git && cd samtools && autoheader &&\
autoconf -Wno-syntax && ./configure && make && sudo make install && \
cd /opt/LoReAn/third_party/software && \
export TOOLDIR=/opt/LoReAn/third_party/software && git clone https://github.com/Gaius-Augustus/Augustus.git &&\
mv Augustus augustus && cd augustus && make clean && make && \
cd /opt/LoReAn/third_party/software && \
tar -zxvf Trinity-v2.5.1.tar.gz && \
mv trinityrnaseq-Trinity-v2.5.1 Trinity &&rm Trinity-v2.5.1.tar.gz && cd Trinity && make && make plugins && \
cd /opt/LoReAn/third_party/software && \
git clone https://github.com/lh3/minimap2.git && cd minimap2 && make && \
cd /opt/LoReAn/third_party/software && \
git clone https://github.com/alexdobin/STAR.git && \
cd /opt/LoReAn/third_party/software && \
tar -zxvf v3.0.1.tar.gz && rm v3.0.1.tar.gz &&\
cd TransDecoder-3.0.1 && make && \
cd /opt/LoReAn/third_party/software && \
tar -zxvf gmap-gsnap-2017-11-15.tar.gz && rm gmap-gsnap-2017-11-15.tar.gz && \
mv gmap-2017-11-15 gmap && cd gmap/ && ./configure && make && sudo make install && \
cd /opt/LoReAn/third_party/software && \
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 && \
cd /opt/LoReAn/third_party/software && \
git clone https://github.com/Gaius-Augustus/BRAKER.git && \
tar -zxvf v1.1.1.tar.gz && rm v1.1.1.tar.gz && \
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 && sudo cpan -f -i File::Which && \
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 && \
cd /opt/LoReAn/third_party/software && \
tar -zxvf genometools-1.5.9.tar.gz && rm genometools-1.5.9.tar.gz && cd genometools-1.5.9 && make && \
cd /opt/LoReAn/third_party/software && \
cp ../../code/createUser.py /usr/local/bin && chmod 775 /usr/local/bin/createUser.py && \
rm /opt/LoReAn/third_party/software/EVidenceModeler-1.1.1/EvmUtils/misc/cufflinks_gtf_to_alignment_gff3.pl && \
sudo chmod -R 775 /opt/LoReAn/code/ && \
tar -pxvzf interproscan-5.27-66.0-64-bit.tar.gz && rm interproscan-5.27-66.0-64-bit.tar.gz && \
cd /opt/LoReAn/third_party/software/interproscan-5.27-66.0 && \
mkdir cddblast && \
mv /opt/LoReAn/third_party/software/ncbi-blast-2.7.1+-x64-linux.tar.gz cddblast/ && \
cd cddblast && tar -zxvf ncbi-blast-2.7.1+-x64-linux.tar.gz && cp -r ncbi-blast-2.7.1+ ../bin/blast && \
cd /opt/LoReAn/third_party/software/interproscan-5.27-66.0 && \
mv /opt/LoReAn/third_party/software/signalp-4.1f.Linux.tar.gz ./ && \
tar -xzf signalp-4.1f.Linux.tar.gz -C bin/signalp/4.1 --strip-components 1 && rm signalp-4.1f.Linux.tar.gz && \
cp signalp-4.1/signalp bin/signalp/4.1/ && \
mkdir /data_panther && \
cd /opt/LoReAn/third_party/software/interproscan-5.27-66.0 && \
mv /opt/LoReAn/third_party/software/tmhmm-2.0c.Linux.tar.gz ./ && \
tar -xzf tmhmm-2.0c.Linux.tar.gz -C ./ && cp tmhmm-2.0c/bin/decodeanhmm.Linux_x86_64 bin/tmhmm/2.0c/decodeanhmm && \
cp tmhmm-2.0c/lib/TMHMM2.0.model data/tmhmm/2.0c/TMHMM2.0c.model && \
cp /opt/LoReAn/third_party/conf_files/interproscan.properties ./interproscan.properties

WORKDIR /usr/local

RUN mkdir nseg && cd nseg && wget ftp://ftp.ncbi.nih.gov/pub/seg/nseg/* && make && mv nseg ../bin && mv nmerge ../bin

COPY RepeatScout-1.0.5.tar.gz ./

RUN tar -xvf RepeatScout* && rm RepeatScout*.tar.gz && mv RepeatScout* RepeatScout && cd RepeatScout && make

RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/2.2.28/ncbi-rmblastn-2.2.28-x64-linux.tar.gz && \
tar -xzvf ncbi-rmblastn* && rm ncbi-rmblastn*.tar.gz && mv ncbi-rmblastn*/bin/rmblastn bin && rm -rf ncbi-rmblastn


RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz && \
tar -xzvf ncbi-blast* && find ncbi-blast* -type f -executable -exec mv {} bin \; && rm -rf ncbi-blast*

RUN sudo perl -MCPAN -e shell && sudo cpan -f -i Text::Soundex

COPY RepeatMasker-open-4-0-7.tar.gz ./

RUN tar -xzvf RepeatMasker-open*.tar.gz \
&& rm -f RepeatMasker-open*.tar.gz && perl -0p -e 's/\/usr\/local\/hmmer/\/usr\/bin/g;' -e 's/\/usr\/local\/rmblast/\/usr\/local\/bin/g;' \
RUN mkdir nseg && cd nseg && wget ftp://ftp.ncbi.nih.gov/pub/seg/nseg/* && make && mv nseg ../bin && mv nmerge ../bin && \
cd /usr/local && \
tar -xvf RepeatScout* && rm RepeatScout*.tar.gz && mv RepeatScout* RepeatScout && cd RepeatScout && make && \
cd /usr/local && \
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/2.2.28/ncbi-rmblastn-2.2.28-x64-linux.tar.gz && \
tar -xzvf ncbi-rmblastn* && rm ncbi-rmblastn*.tar.gz && mv ncbi-rmblastn*/bin/rmblastn bin && rm -rf ncbi-rmblastn && \
cd /usr/local && \
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz && \
tar -xzvf ncbi-blast* && find ncbi-blast* -type f -executable -exec mv {} bin \; && rm -rf ncbi-blast* && \
sudo perl -MCPAN -e shell && sudo cpan -f -i Text::Soundex && \
cd /usr/local && \
tar -xzvf RepeatMasker-open*.tar.gz && \
rm -f RepeatMasker-open*.tar.gz && perl -0p -e 's/\/usr\/local\/hmmer/\/usr\/bin/g;' -e 's/\/usr\/local\/rmblast/\/usr\/local\/bin/g;' \
-e 's/DEFAULT_SEARCH_ENGINE = "crossmatch"/DEFAULT_SEARCH_ENGINE = "ncbi"/g;' \
-e 's/TRF_PRGM = ""/TRF_PRGM = "\/usr\/local\/bin\/trf"/g;' RepeatMasker/RepeatMaskerConfig.tmpl > RepeatMasker/RepeatMaskerConfig.pm

RUN cd /usr/local/RepeatMasker && perl -i -0pe 's/^#\!.*perl.*/#\!\/usr\/bin\/env perl/g' \
RepeatMasker DateRepeats ProcessRepeats RepeatProteinMask DupMasker util/queryRepeatDatabase.pl \
util/queryTaxonomyDatabase.pl util/rmOutToGFF3.pl util/rmToUCSCTables.pl

RUN chmod -R 777 RepeatMasker/

WORKDIR /opt/LoReAn/

RUN apt-get install -y locales && locale-gen en_US.UTF-8 && update-locale

RUN chmod a+w /opt/
-e 's/TRF_PRGM = ""/TRF_PRGM = "\/usr\/local\/bin\/trf"/g;' RepeatMasker/RepeatMaskerConfig.tmpl > RepeatMasker/RepeatMaskerConfig.pm && \
cd /usr/local/RepeatMasker && perl -i -0pe 's/^#\!.*perl.*/#\!\/usr\/bin\/env perl/g' \
RepeatMasker DateRepeats ProcessRepeats RepeatProteinMask DupMasker util/queryRepeatDatabase.pl \
util/queryTaxonomyDatabase.pl util/rmOutToGFF3.pl util/rmToUCSCTables.pl && \
chmod -R 777 RepeatMasker/

WORKDIR /data/

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