docker/cgivar2vcfbed/Dockerfile

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 FROM arvados/jobs
   6 MAINTAINER Jiayong Li <jli@curii.com>
   7
   8 USER root
   9
  10 RUN apt-get update -q
  11
  12 RUN apt-get install -qy build-essential wget cmake zlib1g-dev git
  13
  14 # Installing cgatools 1.8.0
  15
  16 RUN wget https://sourceforge.net/projects/cgatools/files/1.8.0/cgatools-1.8.0.1-linux_binary-x86_64.tar.gz && \
  17     tar -xzvf cgatools-1.8.0.1-linux_binary-x86_64.tar.gz && \
  18     cp cgatools-1.8.0.1-linux_binary-x86_64/bin/cgatools /usr/local/bin
  19
  20 WORKDIR /
  21
  22 # Getting HTSLIB for tabix/bgzip
  23
  24 RUN wget https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.bz2 && \
  25     tar -xjvf htslib-1.3.1.tar.bz2 && \
  26     cd htslib-1.3.1 && ./configure && make && make install
  27
  28 WORKDIR /
  29
  30 # Installing bedtools v2.25.0 and dependencies
  31
  32 RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz && \
  33     tar -xzvf bedtools-2.25.0.tar.gz && \
  34     cd bedtools2/ && make && cp /bedtools2/bin/bedtools /usr/local/bin
  35
  36 WORKDIR /
  37
  38 # Installing gvcf_regions
  39
  40 RUN git clone https://github.com/lijiayong/gvcf_regions