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FROM ubuntu:16.04
RUN apt-get update && \
apt-get install --yes --no-install-recommends \
wget \
g++ \
build-essential \
file \
unzip \
libncurses5-dev \
zlib1g-dev \
libbz2-dev \
liblzma-dev \
libtbb-dev \
git \
libipc-run-perl \
python \
openjdk-8-jre-headless \
bc && \
rm -rf /var/lib/apt/lists/*
ENV reperDir /reper
ENV depDir /dependencies
WORKDIR $reperDir
COPY reper .
COPY reper.conf .
COPY update_exe_path.sh .
COPY scripts/ ./scripts/
ENV PATH="$reperDir":$PATH
WORKDIR $depDir
RUN wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.6/jellyfish-2.2.6.tar.gz && \
tar xzf jellyfish-2.2.6.tar.gz && \
cd jellyfish-2.2.6 && \
./configure && \
make && \
make install && \
cd .. && \
rm -rf jellyfish-2.2.6 jellyfish-2.2.6.tar.gz
ENV LD_LIBRARY_PATH=/usr/local/lib/:$LD_LIBRARY_PATH
RUN wget https://github.com/BenLangmead/bowtie2/releases/download/v2.3.2/bowtie2-2.3.2-linux-x86_64.zip && \
unzip bowtie2-2.3.2-linux-x86_64.zip && \
rm bowtie2-2.3.2-linux-x86_64.zip
ENV PATH="$depDir"/bowtie2-2.3.2:"$PATH"
RUN wget https://github.com/weizhongli/cdhit/releases/download/V4.6.7/cd-hit-v4.6.7-2017-0501-Linux-binary.tar.gz && \
tar xzf cd-hit-v4.6.7-2017-0501-Linux-binary.tar.gz && \
cd cd-hit-v4.6.7-2017-0501 && \
make install && \
cd .. && \
rm -rf cd-hit-v4.6.7-2017-0501 cd-hit-v4.6.7-2017-0501-Linux-binary.tar.gz
RUN wget https://github.com/samtools/samtools/releases/download/1.4.1/samtools-1.4.1.tar.bz2 && \
tar xjf samtools-1.4.1.tar.bz2 && \
cd samtools-1.4.1 && \
./configure && \
make && \
make check && \
make install && \
cd .. && \
rm -rf samtools-1.4.1 samtools-1.4.1.tar.bz2
RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+-x64-linux.tar.gz && \
tar xzf ncbi-blast-2.2.28+-x64-linux.tar.gz && \
rm ncbi-blast-2.2.28+-x64-linux.tar.gz
ENV PATH="$depDir"/ncbi-blast-2.2.28+/bin:"$PATH"
RUN wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.4.0.tar.gz && \
tar xzf Trinity-v2.4.0.tar.gz && \
cd trinityrnaseq-Trinity-v2.4.0 && \
make && \
make plugins && \
cd .. && \
rm Trinity-v2.4.0.tar.gz
ENV TRINITY_HOME="$depDir"/trinityrnaseq-Trinity-v2.4.0
ENV PATH="$TRINITY_HOME":"$PATH"
RUN git clone https://github.com/thackl/kmer-scripts.git
ENV PATH="$depDir"/kmer-scripts/bin/:"$PATH"
WORKDIR $depDir/lib
ENV PERL5LIB="$depDir/lib:$PERL5LIB"
RUN wget http://search.cpan.org/CPAN/authors/id/M/MS/MSCHILLI/Log-Log4perl-1.49.tar.gz && \
tar xzf Log-Log4perl-1.49.tar.gz && \
cd Log-Log4perl-1.49 && \
perl Makefile.PL && \
make && \
make test && \
make install && \
cd .. && \
rm -rf Log-Log4perl-1.49 Log-Log4perl-1.49.tar.gz
RUN wget http://search.cpan.org/CPAN/authors/id/P/PL/PLICEASE/File-Which-1.22.tar.gz && \
tar xzf File-Which-1.22.tar.gz && \
cd File-Which-1.22 && \
perl Makefile.PL && \
make && \
make test && \
make install && \
cd .. && \
rm -rf File-Which-1.22.tar.gz File-Which-1.22
RUN for i in \
https://github.com/BioInf-Wuerzburg/perl5lib-Fastq.git \
https://github.com/BioInf-Wuerzburg/perl5lib-Fasta.git \
https://github.com/thackl/perl5lib-Jellyfish.git \
https://github.com/thackl/perl5lib-Kmer.git \
https://github.com/BioInf-Wuerzburg/perl5lib-Verbose.git \
https://github.com/thackl/perl5lib-Sam.git; \
do \
git clone ${i} gitclone && \
mv gitclone/lib/* . && \
rm -rf gitclone; \
done
# update the path in reper.conf
RUN /reper/update_exe_path.sh /reper/reper.conf
WORKDIR /data
RUN chmod -R a+rwX $reperDir
ENTRYPOINT ["reper"]