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FROM jupyter/datascience-notebook:160eb5183ace
LABEL maintainer="Genomics Division, ITER (genomicsITER)"
USER root
WORKDIR /home/jovyan/software
RUN apt-get update && \
apt-get install -y \
autoconf \
zlib1g-dev \
cmake \
default-jre \
unzip \
apt-transport-https \
python2.7 \
python-pip \
strace \
libhdf5-cpp-11 \
libbz2-dev \
liblzma-dev ncurses-dev libncurses5-dev libncursesw5-dev \
python3 python3-setuptools libboost-all-dev \
python3-h5py python3-numpy python3-dateutil python3-progressbar \
libboost-filesystem1.58.0 libboost-program-options1.58.0 \
libboost-system1.58.0 libboost-log1.58.0 libboost-thread1.58.0 \
libboost-python1.58.0 graphviz parallel
RUN pip install bash_kernel biopython nanosim-h jupyterlab HTSeq && \
python -m bash_kernel.install
RUN echo '**************************************' && \
echo '*******Installing minimap2 ***********' && \
echo '**************************************' && \
git clone https://github.com/lh3/minimap2 && \
cd minimap2 && make && \
find . -name '*.o' -exec rm -f {} \; && \
cd ..
RUN echo '**************************************' && \
echo '*******Installing racon ***********' && \
echo '**************************************' && \
git clone --recursive https://github.com/isovic/racon.git racon && \
cd racon && mkdir build && cd build && \
cmake -DCMAKE_BUILD_TYPE=Release .. && \
make && \
find . -name '*.o' -exec rm -f {} \;
RUN echo '**************************************' && \
echo '*******Installing Unicycler **********' && \
echo '**************************************' && \
git clone https://github.com/rrwick/Unicycler.git && \
cd Unicycler && make && \
find . -name '*.o' -exec rm -f {} \; && \
cd ..
RUN echo '**************************************' && \
echo '*******Installing miniasm ************' && \
echo '**************************************' && \
git clone https://github.com/lh3/miniasm && \
(cd miniasm && make && find . -name '*.o' -exec rm -f {} \;)
RUN echo '**************************************' && \
echo '*******Installing canu ***************' && \
echo '**************************************' && \
git clone https://github.com/marbl/canu.git && \
cd canu/src && make -j 1 && find . -name '*.o' -exec rm -f {} \;
RUN echo '**************************************' && \
echo '*******Installing quast **************' && \
echo '**************************************' && \
git clone https://github.com/ablab/quast.git && \
cd quast && ./setup.py install && \
find . -name '*.o' -exec rm -f {} \; && \
cd ..
RUN echo '**************************************' && \
echo '*******Installing Porechop ***********' && \
echo '**************************************' && \
git clone https://github.com/rrwick/Porechop.git && \
cd Porechop && \
python3 setup.py install && \
find . -name '*.o' -exec rm -f {} \;
RUN echo '**************************************' && \
echo '*******Installing Rebaler ************' && \
echo '**************************************' && \
git clone https://github.com/rrwick/Rebaler.git && \
cd Rebaler && \
python3 setup.py install
RUN echo '***********************************' && \
echo '*******Installing samtools *******' && \
echo '***********************************' && \
wget "https://sourceforge.net/projects/samtools/files/samtools/1.5/samtools-1.5.tar.bz2" && \
tar -xvjf samtools-1.5.tar.bz2 && rm samtools-1.5.tar.bz2 && \
cd samtools-1.5 && autoheader && autoconf -Wno-syntax && \
./configure && make && make install && cd ..
RUN echo '***********************************' && \
echo '*******Installing SPAdes *******' && \
echo '***********************************' && \
wget "http://cab.spbu.ru/files/release3.13.0/SPAdes-3.13.0-Linux.tar.gz" && \
tar -xvzf SPAdes-3.13.0-Linux.tar.gz && rm SPAdes-3.13.0-Linux.tar.gz
RUN echo '***********************************' && \
echo '*******Installing pilon ***********' && \
echo '***********************************' && \
mkdir pilon && cd pilon && \
wget "https://github.com/broadinstitute/pilon/releases/download/v1.22/pilon-1.22.jar" && \
chown jovyan pilon-1.22.jar && cd ..
RUN echo '***********************************' && \
echo '*******Installing bwa *************' && \
echo '***********************************' && \
wget "https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.15.tar.bz2" && \
tar -xvjf bwa-0.7.15.tar.bz2 && \
rm bwa-0.7.15.tar.bz2 && \
cd bwa-0.7.15 && make && \
find . -name '*.o' -exec rm -f {} \; && \
cd ..
RUN echo '***********************************' && \
echo '*******Installing ncbi-blast+ *****' && \
echo '***********************************' && \
wget "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-x64-linux.tar.gz” && \
tar zxvpf ncbi-blast-2.7.1+-x64-linux.tar.gz && \
rm ncbi-blast-2.7.1+-x64-linux.tar.gz
RUN echo '***********************************' && \
echo '*******Installing MaSuRCA *********' && \
echo '***********************************' && \
wget "https://github.com/alekseyzimin/masurca/releases/download/3.2.8/MaSuRCA-3.2.8.tar.gz" && \
tar -xzvf MaSuRCA-3.2.8.tar.gz && \
rm MaSuRCA-3.2.8.tar.gz && \
cd MaSuRCA-3.2.8 && ./install.sh && \
PERL_MM_USE_DEFAULT=1 perl -MCPAN -e 'install Statistics::Descriptive' && \
find . -name '*.o' -exec rm -f {} \; && \
cd ..
RUN echo '*********************************************' && \
echo '*******Installing rhdf5 (R bioconductor) ****' && \
echo '*********************************************' && \
echo 'local({r <- getOption("repos"); r["CRAN"] <- "http://cran.cnr.berkeley.edu/"; options(repos = r)})' >> /home/jovyan/.Rprofile && \
R -e "source('http://www.bioconductor.org/biocLite.R'); biocLite('rhdf5'); install.packages(c('shiny','svDialogs','data.table','bit64'))"
RUN echo '***********************************' && \
echo '*******Installing Flye ************' && \
echo '***********************************' && \
wget "https://codeload.github.com/fenderglass/Flye/tar.gz/2.3.6" && \
tar -xzvf 2.3.6 && \
rm 2.3.6 && \
cd Flye-2.3.6 && \
python2 setup.py install && cd ..
RUN echo '***********************************' && \
echo '*******Installing nanopolish ******' && \
echo '***********************************' && \
git clone --recursive https://github.com/jts/nanopolish.git && \
cd nanopolish && \
make && \
find . -name '*.o' -exec rm -f {} \; && \
cd ..
RUN echo '***********************************' && \
echo '*******Installing bowtie2 *********' && \
echo '***********************************' && \
wget "https://sourceforge.net/projects/bowtie-bio/files/bowtie2-2.3.4.1-linux-x86_64.zip" && \
unzip bowtie2-2.3.4.1-linux-x86_64.zip -d ~/software && \
rm bowtie2-2.3.4.1-linux-x86_64.zip
RUN echo '****************************************************' && \
echo '*******Installing albacore & fast5 (ONT software) **' && \
echo '****************************************************' && \
wget -O- https://mirror.oxfordnanoportal.com/apt/ont-repo.pub | apt-key add - && \
echo "deb http://mirror.oxfordnanoportal.com/apt xenial-stable non-free" | tee /etc/apt/sources.list.d/nanoporetech.sources.list && \
apt-get update && \
wget -qO python3-ont-albacore_2.3.3-1~xenial_amd64.deb https://mirror.oxfordnanoportal.com/software/analysis/python3-ont-albacore_2.3.3-1~xenial_amd64.deb && \
apt-get install -y python3-ont-fast5-api && \
dpkg -i python3-ont-albacore_2.3.3-1~xenial_amd64.deb && \
rm python3-ont-albacore_2.3.3-1~xenial_amd64.deb && \
apt-get install -fy && \
apt-get -y install gnuplot-x11 qt5-default
RUN echo '***********************************' && \
echo '*******Installing Bandage *********' && \
echo '***********************************' && \
mkdir Bandage && cd Bandage && \
wget "https://github.com/rrwick/Bandage/releases/download/v0.8.1/Bandage_Ubuntu_dynamic_v0_8_1.zip" && \
unzip Bandage_Ubuntu_dynamic_v0_8_1.zip && \
rm Bandage_Ubuntu_dynamic_v0_8_1.zip
RUN echo '***********************************' && \
echo '*******Installing Nanosim *********' && \
echo '***********************************' && \
wget "https://github.com/bcgsc/NanoSim/archive/v2.1.0.tar.gz" && \
tar -xzvf v2.1.0.tar.gz && \
rm v2.1.0.tar.gz
ENV PATH "$PATH:/home/jovyan/software/ncbi-blast-2.7.1+/bin"
ENV PATH "$PATH:/home/jovyan/software/Porechop"
ENV PATH "$PATH:/home/jovyan/software/SPAdes-3.13.0-Linux/bin"
ENV PATH "$PATH:/home/jovyan/software/minimap2"
ENV PATH "$PATH:/home/jovyan/software/racon/build/bin"
ENV PATH "$PATH:/home/jovyan/software/bowtie2-2.3.4.1-linux-x86_64"
ENV PATH "$PATH:/home/jovyan/software/samtools-1.5"
ENV PATH "$PATH:/home/jovyan/software/pilon/bin"
ENV PATH "$PATH:/home/jovyan/software/Unicycler"
ENV PATH "$PATH:/home/jovyan/software/bwa-0.7.15"
ENV PATH "$PATH:/home/jovyan/software/canu/Linux-amd64/bin"
ENV PATH "$PATH:/home/jovyan/software/quast"
ENV PATH "$PATH:/home/jovyan/software/miniasm"
ENV PATH "$PATH:/home/jovyan/software/pilon"
ENV PATH "$PATH:/home/jovyan/software/Flye-2.3.6/bin"
ENV PATH "$PATH:/home/jovyan/software/nanopolish"
ENV PATH "$PATH:/home/jovyan/software/MaSuRCA-3.2.8/bin"
ENV PATH "$PATH:/home/jovyan/software/Bandage"
ENV PATH "$PATH:/home/jovyan/software/NanoSim-2.1.0/src"
USER jovyan
WORKDIR /home/jovyan/notebooks
CMD jupyter lab --allow-root