Dockerfile

FROM mobinasri/bio_base:v0.4.0
MAINTAINER Mobin Asri, masri@ucsc.edu

RUN mkdir -p /home/apps
RUN pip3 install scipy pandas matplotlib
RUN apt-get update && apt-get install -y build-essential python3-dev autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev wget unzip vim


#install Java
RUN cd /home/apps && \
    wget https://download.oracle.com/java/23/latest/jdk-23_linux-x64_bin.tar.gz && \
    tar -xvzf jdk-23_linux-x64_bin.tar.gz
ENV PATH=$PATH:/home/apps/jdk-23.0.1/bin

#intstall IGV
RUN cd /home/apps && \
    wget https://data.broadinstitute.org/igv/projects/downloads/2.11/IGV_2.11.3.zip &&\
    unzip IGV_2.11.3.zip
ENV PATH=$PATH:/home/apps/IGV_2.11.3

#install sonLib
RUN cd /home/apps && \
    git clone https://github.com/benedictpaten/sonLib && \
    cd sonLib && \
    make

#install hstlib  C API
RUN cd /home/apps && \
    wget https://github.com/samtools/htslib/releases/download/1.13/htslib-1.13.tar.bz2 && \
    tar -xvjf htslib-1.13.tar.bz2 && \
    cd htslib-1.13 && \
    autoreconf -i && \
    ./configure && \
    make && \
    make install
ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib

#install tabix
RUN apt-get install -y tabix 

#install whatshap
ENV LANG="C.UTF-8" 
RUN pip3 install cython && pip3 install whatshap

RUN cd /home/apps && \
     git clone https://sourceware.org/git/valgrind.git && \
     cd valgrind && \
     ./autogen.sh  && \
     ./configure && \
     make && \
     make install

RUN apt-get update
RUN apt-get install -y libc6-dbg gdb
RUN pip install smt #https://smt.readthedocs.io/en/latest/_src_docs/applications/ego.html
RUN cd /home/apps && \
    wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig && \
    chmod 777 bedGraphToBigWig

COPY ./programs /home/programs
# Add cigar_it to the submodules dir
COPY ./ext/secphase/programs/submodules/cigar_it /home/programs/submodules/cigar_it
COPY ./scripts  /home/scripts
RUN cd /home/programs && make
ENV PATH="$PATH:/home/programs/bin:/home/apps"


ENV CALC_MEAN_SD_PY=/home/programs/src/calc_mean_sd.py
ENV CALC_MODE_SD_PY=/home/programs/src/calc_mode_sd.py
ENV FIT_MODEL_PY=/home/programs/src/fit_model.py
ENV PROJECT_BLOCKS_PY=/home/programs/src/project_blocks.py
ENV PROJECT_BLOCKS_MULTI_THREADED_PY=/home/programs/src/project_blocks_multi_thread.py
ENV FIT_GMM_PY=/home/programs/src/fit_gmm.py
ENV PDF_GENERATOR_PY=/home/programs/src/pdf_generator.py
ENV SPLIT_BED_CONTIG_WISE_PY=/home/programs/src/split_bed_contig_wise.py


## UCSC convention is to work in /data
RUN mkdir -p /data
WORKDIR /data