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Dockerfile
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# An example of extension of the jupyter stack 'datascience-notebook'
# with pip modules ('pip install ...') and their system dependencies ('apt-get install -y ...')
FROM jupyter/datascience-notebook
USER root
RUN DEBIAN_FRONTEND=noninteractive apt-get update -y
RUN DEBIAN_FRONTEND=noninteractive apt-get install -y apt-utils python3-pyqt5 pyqt5-dev-tools qttools5-dev-tools gnupg2
RUN DEBIAN_FRONTEND=noninteractive apt-get install -y unzip wget build-essential cmake git-all tar gzip
RUN DEBIAN_FRONTEND=noninteractive apt-get install -y minimap2 seqtk bedtools vcftools bcftools assemblytics bandage
RUN wget -O- https://mirror.oxfordnanoportal.com/apt/ont-repo.pub | apt-key add -
RUN echo 'deb http://mirror.oxfordnanoportal.com/apt focal-stable non-free' | tee /etc/apt/sources.list.d/nanoporetech.sources.list
RUN apt-get update
RUN apt-get install -y ont-guppy-cpu
ENV JUPYTER_ENABLE_LAB=yes
ENV PYTHONPATH="/usr/bin/python3.8"
RUN python3 -m pip install matplotlib pandas sniffles
RUN python3 -m pip install PyQt5 ete3 owlready2 pyproteinsExt ipympl jupyterlab
RUN python3 -m pip install --upgrade ipython
RUN python3 -m pip install bash_kernel
RUN python3 -m bash_kernel.install
#RUN python3 -m pip install medaka
RUN python3 -m pip install duplex-tools
RUN python3 -m pip install medaka
RUN conda update --all --yes
RUN conda config --add channels defaults
RUN conda config --add channels bioconda
RUN conda config --add channels conda-forge
RUN conda create -n flye --no-default-packages
RUN conda install flye=2.9 -n flye
RUN conda clean --all --yes
RUN conda create -n nanocomp --no-default-packages
RUN conda install nanocomp -n nanocomp
RUN conda clean --all --yes
RUN conda create -n raven-assembler --no-default-packages
RUN conda install raven-assembler -n raven-assembler
RUN conda clean --all --yes
RUN conda create -n ragtag --no-default-packages
RUN conda install ragtag -n ragtag
RUN conda clean --all --yes
RUN conda create -n mummer4 --no-default-packages
RUN conda install mummer4 -n mummer4
RUN conda clean --all --yes
RUN conda create -n racon --no-default-packages
RUN conda install racon -n racon
RUN conda clean --all --yes
RUN conda create -n assembly-stats --no-default-packages
RUN conda install assembly-stats -n assembly-stats
RUN conda clean --all --yes
RUN conda create -n nanoplot --no-default-packages
RUN conda install nanoplot -n nanoplot
RUN conda clean --all --yes
RUN conda create -n quast --no-default-packages
RUN conda install python=3.7 quast -n quast
RUN conda clean --all --yes
RUN conda create -n blobtools --no-default-packages
RUN conda install blobtools pysam -n blobtools
RUN conda clean --all --yes
#RUN conda create -n kraken2 --no-default-packages
#RUN conda install kraken2 -n kraken2
#RUN conda clean --all --yes
#RUN conda create -n porechop --no-default-packages
#RUN conda install porechop -n porechop
#RUN conda clean --all --yes
RUN conda create -n diamond --no-default-packages
RUN conda install diamond -n diamond
RUN conda clean --all --yes
#RUN conda create -n blast --no-default-packages
#RUN conda install blast -n blast
#RUN conda clean --all --yes
#RUN conda create -n sourmash --no-default-packages
#RUN conda install sourmash -n sourmash
#RUN conda clean --all --yes
#RUN conda create -n kaiju --no-default-packages
#RUN conda install kaiju -n kaiju
#RUN conda clean --all --yes
#RUN conda create -n krona --no-default-packages
#RUN conda install krona -n krona
#RUN conda clean --all --yes
#RUN conda create -n spades --no-default-packages
#RUN conda install spades -n spades
#RUN conda clean --all --yes
#RUN conda create -n checkv --no-default-packages
#RUN conda install checkv -n checkv
#RUN conda clean --all --yes
RUN conda create -n syri_env --no-default-packages
RUN conda install syri -n syri_env
RUN conda install plotsr -n syri_env
RUN conda clean --all --yes
RUN mkdir -p /opt
RUN cd /opt
RUN wget https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2 && \
tar jxf samtools-1.11.tar.bz2 && \
rm samtools-1.11.tar.bz2 && \
cd samtools-1.11 && \
./configure && \
make && \
make install
RUN conda create -n busco --no-default-packages
RUN conda install r-plyr -n busco
RUN conda install busco=5.5.0 -n busco
RUN conda clean --all --yes
#ENV PATH="${PATH}:/opt/conda/envs/:/opt/conda/envs/assembly-stats/bin:/opt/conda/envs/blobtools/bin:/opt/conda/envs/flye/bin:/opt/conda/envs/kraken2/bin:/opt/conda/envs/mummer4/bin:/opt/conda/envs/nanoplot/bin:/opt/conda/envs/quast/bin:/opt/conda/envs/ragtag/bin:/opt/conda/envs/sourmash/bin:/opt/conda/envs/blast/bin:/opt/conda/envs/diamond/bin:/opt/conda/envs/kaiju/bin:/opt/conda/envs/krona/bin:/opt/conda/envs/nanocomp/bin:/opt/conda/envs/porechop/bin:/opt/conda/envs/racon/bin:/opt/conda/envs/raven-assembler/bin:/opt/conda/envs/spades/bin:/opt/conda/envs/checkv/bin:/opt/conda/envs/medaka/bin"
ENV PATH="${PATH}:/opt/conda/envs/:/opt/conda/envs/assembly-stats/bin:/opt/conda/envs/blobtools/bin:/opt/conda/envs/flye/bin:/opt/conda/envs/mummer4/bin:/opt/conda/envs/nanoplot/bin:/opt/conda/envs/quast/bin:/opt/conda/envs/ragtag/bin:/opt/conda/envs/diamond/bin:/opt/conda/envs/nanocomp/bin:/opt/conda/envs/racon/bin:/opt/conda/envs/raven-assembler/bin:/opt/conda/envs/syri_env/bin:/opt/conda/envs/busco/bin"
#/opt/conda/envs/medaka/bin
ENV export PATH="$PATH:/opt/samtools-1.11"
ENV CPATH="${CPATH}:/opt/conda/envs/busco/include"
#Dedicated install to ONT analyses, unpacked
#RUN mkdir -p /opt/
## bwa mem2
#RUN mkdir -p /opt/bwa-mem2
#RUN cd /opt/bwa-mem2 && curl -L https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2/bwa-mem2-2.0pre2_x64-linux.tar.bz2 | tar jxf -
#RUN ln -s /opt/bwa-mem2/bwa-mem2-2.0pre2_x64-linux/bwa-mem2.avx2 /usr/bin/bwa-mem2