docker/vcfutil/Dockerfile

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 <<<<<<< HEAD
   6 =======
   7 # build instruction:
   8 # docker build -t dockername --file=/path/to/lightning/docker/vcfutil/Dockerfile /path/to/lightning
   9
  10
  11 >>>>>>> 20765-moving-gvcf-regions
  12 FROM python:3.11-buster
  13
  14 USER root
  15
  16 RUN apt-get update -q
  17
  18 RUN apt-get install -qy build-essential wget cmake zlib1g-dev \
  19     libbz2-dev liblzma-dev libncurses5-dev libncursesw5-dev git vcftools
  20
  21 # Setting up gvcf_region
  22 COPY ./gvcf_regions /gvcf_regions
  23
  24 # Getting HTSLIB 1.9 for tabix/bgzip
  25
  26 RUN wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 && tar -xjvf htslib-1.9.tar.bz2 && \
  27     cd htslib-1.9 && ./configure && make && make install
  28
  29 WORKDIR /
  30
  31 # Installing samtools 1.9
  32
  33 RUN wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 && tar -xjvf samtools-1.9.tar.bz2 && \
  34     cd samtools-1.9 && ./configure && make && make install
  35
  36 WORKDIR /
  37
  38 # Installing bcftools 1.9
  39
  40 RUN wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2 && tar -xjvf bcftools-1.9.tar.bz2 && \
  41     cd bcftools-1.9 && ./configure && make && make install
  42
  43 WORKDIR /
  44
  45 # Installing rtg tools v3.8.4
  46
  47 RUN apt-get install -qy unzip
  48
  49 RUN wget https://github.com/RealTimeGenomics/rtg-tools/releases/download/3.9.1/rtg-tools-3.9.1-linux-x64.zip && \
  50     unzip rtg-tools-3.9.1-linux-x64.zip && \
  51     cd rtg-tools-3.9.1 && ./rtg help
  52
  53 ENV PATH="/rtg-tools-3.9.1:${PATH}"
  54
  55 WORKDIR /
  56
  57 # Installing bedops v2.4.35
  58
  59 RUN wget https://github.com/bedops/bedops/releases/download/v2.4.35/bedops_linux_x86_64-v2.4.35.tar.bz2 && \
  60     tar jxvf bedops_linux_x86_64-v2.4.35.tar.bz2 && \
  61     cp bin/* /usr/local/bin
  62
  63 WORKDIR /
  64
  65 # Installing bedtools 2.27.1
  66
  67 RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedtools-2.27.1.tar.gz && \
  68     tar -xzvf bedtools-2.27.1.tar.gz && \
  69     cd bedtools2 && make && cp bin/* /usr/local/bin