docker/vcfutil/Dockerfile

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 FROM python:3.8-buster
   6
   7 USER root
   8
   9 RUN apt-get update -q
  10
  11 RUN apt-get install -qy build-essential wget cmake zlib1g-dev \
  12     libbz2-dev liblzma-dev libncurses5-dev libncursesw5-dev git vcftools
  13
  14 # Getting HTSLIB 1.9 for tabix/bgzip
  15
  16 RUN wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 && tar -xjvf htslib-1.9.tar.bz2 && \
  17     cd htslib-1.9 && ./configure && make && make install
  18
  19 WORKDIR /
  20
  21 # Installing samtools 1.9
  22
  23 RUN wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 && tar -xjvf samtools-1.9.tar.bz2 && \
  24     cd samtools-1.9 && ./configure && make && make install
  25
  26 WORKDIR /
  27
  28 # Installing bcftools 1.9
  29
  30 RUN wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2 && tar -xjvf bcftools-1.9.tar.bz2 && \
  31     cd bcftools-1.9 && ./configure && make && make install
  32
  33 WORKDIR /
  34
  35 # Installing rtg tools v3.8.4
  36
  37 RUN apt-get install -qy unzip
  38
  39 RUN wget https://github.com/RealTimeGenomics/rtg-tools/releases/download/3.9.1/rtg-tools-3.9.1-linux-x64.zip && \
  40     unzip rtg-tools-3.9.1-linux-x64.zip && \
  41     cd rtg-tools-3.9.1 && ./rtg help
  42
  43 ENV PATH="/rtg-tools-3.9.1:${PATH}"
  44
  45 WORKDIR /
  46
  47 # Installing bedops v2.4.35
  48
  49 RUN wget https://github.com/bedops/bedops/releases/download/v2.4.35/bedops_linux_x86_64-v2.4.35.tar.bz2 && \
  50     tar jxvf bedops_linux_x86_64-v2.4.35.tar.bz2 && \
  51     cp bin/* /usr/local/bin
  52
  53 WORKDIR /
  54
  55 # Installing bedtools 2.27.1
  56
  57 RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedtools-2.27.1.tar.gz && \
  58     tar -xzvf bedtools-2.27.1.tar.gz && \
  59     cd bedtools2 && make && cp bin/* /usr/local/bin
  60
  61 WORKDIR /
  62
  63 # Installing gvcf_regions
  64
  65 RUN git clone https://github.com/acoleman2000/gvcf_regions