docker/vcfutil/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 \
  13     libbz2-dev liblzma-dev libncurses5-dev libncursesw5-dev git vcftools
  14
  15 # Getting HTSLIB 1.9 for tabix/bgzip
  16
  17 RUN wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 && tar -xjvf htslib-1.9.tar.bz2 && \
  18     cd htslib-1.9 && ./configure && make && make install
  19
  20 WORKDIR /
  21
  22 # Installing samtools 1.9
  23
  24 RUN wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 && tar -xjvf samtools-1.9.tar.bz2 && \
  25     cd samtools-1.9 && ./configure && make && make install
  26
  27 WORKDIR /
  28
  29 # Installing bcftools 1.9
  30
  31 RUN wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2 && tar -xjvf bcftools-1.9.tar.bz2 && \
  32     cd bcftools-1.9 && ./configure && make && make install
  33
  34 WORKDIR /
  35
  36 # Installing rtg tools v3.8.4
  37
  38 RUN apt-get install -qy unzip
  39
  40 RUN wget https://github.com/RealTimeGenomics/rtg-tools/releases/download/3.9.1/rtg-tools-3.9.1-linux-x64.zip && \
  41     unzip rtg-tools-3.9.1-linux-x64.zip && \
  42     cd rtg-tools-3.9.1 && ./rtg help
  43
  44 ENV PATH="/rtg-tools-3.9.1:${PATH}"
  45
  46 WORKDIR /
  47
  48 # Installing bedops v2.4.35
  49
  50 RUN wget https://github.com/bedops/bedops/releases/download/v2.4.35/bedops_linux_x86_64-v2.4.35.tar.bz2 && \
  51     tar jxvf bedops_linux_x86_64-v2.4.35.tar.bz2 && \
  52     cp bin/* /usr/local/bin
  53
  54 WORKDIR /
  55
  56 # Installing bedtools 2.27.1
  57
  58 RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedtools-2.27.1.tar.gz && \
  59     tar -xzvf bedtools-2.27.1.tar.gz && \
  60     cd bedtools2 && make && cp bin/* /usr/local/bin
  61
  62 WORKDIR /
  63
  64 # Installing gvcf_regions
  65
  66 RUN git clone https://github.com/lijiayong/gvcf_regions