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FROM ipython/scipystack | |
MAINTAINER Zichen Wang <zichen.wang@mssm.edu> | |
# Copy the application folder inside the container | |
ADD . /notebook | |
# Set the default directory where CMD will execute | |
WORKDIR /notebook | |
# Set environment variable | |
ENV HOME /notebook | |
# Install additional python packages | |
RUN pip2 install -r requirements.txt | |
# Install wget and unzip | |
RUN apt-get update -qq && apt-get install -y \ | |
wget \ | |
unzip \ | |
# Install java for fastQC | |
default-jre \ | |
# Install R | |
r-base \ | |
r-base-dev \ | |
&& rm -rf /var/lib/apt/lists/* | |
# Install R pacakges | |
RUN R -e 'source("http://bioconductor.org/biocLite.R"); biocLite("edgeR");' | |
# Install SRA-tookit, fastQC, STAR, featureCounts | |
RUN wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.6.2/sratoolkit.2.6.2-ubuntu64.tar.gz | |
RUN tar zxvf sratoolkit.2.6.2-ubuntu64.tar.gz | |
RUN ln -s /notebook/sratoolkit.2.6.2-ubuntu64/bin/* /usr/local/bin/ | |
RUN wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip | |
RUN unzip fastqc_v0.11.5.zip | |
RUN chmod 755 FastQC/fastqc && ln -s /notebook/FastQC/fastqc /usr/local/bin/ | |
RUN wget https://github.com/alexdobin/STAR/archive/STAR_2.4.1c.tar.gz | |
RUN tar zxvf STAR_2.4.1c.tar.gz | |
RUN cd STAR-STAR_2.4.1c/source && make STAR | |
RUN ln -s /notebook/STAR-STAR_2.4.1c/bin/Linux_x86_64/STAR /usr/local/bin/ | |
RUN wget -O subread-1.4.6-p2-Linux-x86_64.tar.gz --no-check-certificate https://sourceforge.net/projects/subread/files/subread-1.4.6-p2/subread-1.4.6-p2-Linux-x86_64.tar.gz | |
RUN tar zxvf subread-1.4.6-p2-Linux-x86_64.tar.gz | |
RUN ln -s /notebook/subread-1.4.6-p2-Linux-x86_64/bin/* /usr/local/bin/ | |
# Clean-ups | |
RUN rm *.gz && rm *.zip | |
# Expose port | |
EXPOSE 8888 | |
ADD notebook.sh / | |
# Start notebook server | |
CMD ["/notebook.sh"] |