--- /dev/null
+FROM arvados/jobs:latest
+USER root
+
+# Install python tools
+RUN apt-get update && apt-get install -y --no-install-recommends apt-utils
+RUN apt-get install -y apt-utils && apt-get install -y unzip
+RUN apt-get install autoconf -y
+RUN apt-get install wget -y
+RUN apt-get install python-pip -y
+RUN apt-get install python-numpy -y && apt-get install python-scipy -y
+RUN apt-get install python-matplotlib -y && apt-get install python-pandas -y
+RUN apt-get upgrade -y
+RUN apt-get clean
+
+# install lib files to build SAMtools
+RUN apt-get install libncurses5-dev -y && apt-get install libbz2-dev -y && apt-get install liblzma-dev -y && apt-get install git -y && apt-get install autoconf -y
+
+# installing zlib1g
+RUN apt-get install zlib1g-dev -y
+RUN apt-get install zlib1g -y
+
+# Installing xz-utils
+
+RUN apt-get install xz-utils -y
+
+# Installing liblzma-dev
+RUN apt-get install liblzma-dev -y
+
+# Installing pthreads
+RUN apt-get install libpthread-stubs0-dev -y
+
+# Installing libcurl
+RUN apt-get install libcurl3-openssl-dev -y
+
+# Installing libcrypto
+RUN apt-get install libssl-dev -y
+
+# Installing bc
+RUN apt-get install bc -y
+
+# installing build essentials
+RUN apt-get install build-essential -y
+
+# Installing parallel
+RUN apt-get install parallel -y
+
+# Installing Cmake
+RUN apt-get install cmake -y
+
+# Installing SDSL
+RUN cd /tmp && git clone 'https://github.com/simongog/sdsl-lite.git' && cd sdsl-lite && ./install.sh /usr/local
+
+RUN apt-get remove libhts-dev
+
+# Installing htslib
+RUN cd /tmp && wget http://github.com/samtools/htslib/archive/1.10.2.zip && unzip 1.10.2 && cd htslib-1.10.2 && make && make install && cd /tmp && rm -rf htslib-1.10.2 && ldconfig
+
+# Installing bcftools
+
+RUN wget http://github.com/samtools/bcftools/archive/1.10.2.zip && unzip 1.10.2 && cd bcftools-1.10.2 && autoheader && autoconf && ./configure && make && make install
projects / arvados-tutorial.git / blobdiff