X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/aa289173560cd4466d890f3a63927650e37d8aa7..cec9a7f6a83fc2596e042e8adc6179b202f92a6e:/docker/bam2fastq/Dockerfile

diff --git a/docker/bam2fastq/Dockerfile b/docker/bam2fastq/Dockerfile
deleted file mode 100644
index d40b3fa..0000000
--- a/docker/bam2fastq/Dockerfile
+++ /dev/null
@@ -1,67 +0,0 @@
-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 samtools
-
-RUN wget http://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2 && tar -xvf samtools-1.10.tar.bz2 && cd samtools-1.10 && autoheader && autoconf && ./configure && make && make install 
-
-RUN git clone --recursive https://github.com/jts/bam2fastq
-WORKDIR /bam2fastq
-RUN make
-
-WORKDIR /
-