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#################################################################
# Dockerfile of BGDMdocker
#
# Version: 1.0
# Software: prokka,panX&antismash
# Software Version: 1.12,1.0,3.0.5.1
# Description: BGDMdocker: an workflow base on Docker for analysis and visualization pan-genome and biosynthetic gene clusters of Bacterial
# Code: https://github.com/cgwyx/BGDMdocker
# Base Image: debian:latest
# Build Cmd: sudo docker build -t BGDMdocker:latest .
# Pull Cmd: docker pull BGDMdocker:latest
# Run Cmd: sudo docker run -it --rm -v /home:/home -p 8000:8000 --name=BGDMdocker BGDMdocker:latest
# File Author / Maintainer: cheng gong <512543469@qq.com>
#################################################################
FROM antismash/standalone-lite:4.0.0
MAINTAINER cheng gong <512543469@qq.com>
ENV ANTISMASH_URL="https://dl.secondarymetabolites.org/releases"
ENV ANTISMASH_VERSION="4.0.0"
# Grab the databases
WORKDIR /antismash-${ANTISMASH_VERSION}
RUN python download_databases.py
ADD instance.cfg antismash/config/instance.cfg
#######miniconda##########
WORKDIR /
ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
RUN apt-get update --fix-missing && apt-get install -y wget bzip2 ca-certificates \
libglib2.0-0 libxext6 libsm6 libxrender1 \
git mercurial subversion
RUN echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
wget --quiet https://repo.continuum.io/miniconda/Miniconda2-4.3.14-Linux-x86_64.sh -O ~/miniconda.sh && \
/bin/bash ~/miniconda.sh -b -p /opt/conda && \
rm ~/miniconda.sh
RUN apt-get install -y curl grep sed dpkg && \
TINI_VERSION=`curl https://github.com/krallin/tini/releases/latest | grep -o "/v.*\"" | sed 's:^..\(.*\).$:\1:'` && \
curl -L "https://github.com/krallin/tini/releases/download/v${TINI_VERSION}/tini_${TINI_VERSION}.deb" > tini.deb && \
dpkg -i tini.deb && \
rm tini.deb && \
apt-get clean
ENV PATH /opt/conda/bin:$PATH
#######prokka##########
RUN conda update --all -y &&\
conda config --add channels r &&\
conda config --add channels bioconda &&\
conda config --set show_channel_urls yes &&\
conda install -y prokka=1.12
##########pan-genome-analysis############
RUN conda update --all -y &&\
conda config --add channels r &&\
conda config --add channels bioconda &&\
conda config --add channels conda-forge &&\
#conda config --add channels defaults &&\
#conda config --set show_channel_urls yes
git clone https://github.com/neherlab/pan-genome-analysis.git &&\
cd pan-genome-analysis &&\
git submodule update --init &&\
conda install -y python=2.7.13 biopython=1.66 numpy=1.10.4 scipy=0.16.1 pandas=0.16.2 ete2=2.3.10 diamond=0.8.36 fasttree=2.1.9 mafft=7.305 mcl=14.137 raxml=8.2.9
##########pan-genome-visualization############
RUN conda install nodejs=4.4.1 &&\
git clone https://github.com/neherlab/pan-genome-visualization.git &&\
cd pan-genome-visualization && \
git submodule update --init && \
npm install
ADD ./panx-docker-add-new-pages-repo.sh / \
./panx-docker-link-to-server.py /
#Expose port 8000 (webserver)
EXPOSE :8000
WORKDIR /pan-genome-analysis
CMD ["/bin/bash"]