1 # Copyright (C) The Lightning Authors. All rights reserved.
3 # SPDX-License-Identifier: AGPL-3.0
6 MAINTAINER Jiayong Li <jli@curii.com>
9 RUN apt-get update --fix-missing -qy
11 RUN apt-get install -qy wget \
25 RUN apt-get update && \
26 apt-get install -y openjdk-8-jdk && \
27 apt-get install -y ant && \
30 #Fixing certificate issues
31 RUN apt-get update && \
32 apt-get install ca-certificates-java && \
34 update-ca-certificates -f
37 RUN wget https://faculty.washington.edu/browning/beagle/beagle.05May22.33a.jar
38 RUN wget https://faculty.washington.edu/browning/beagle/bref3.05May22.33a.jar
40 # Getting HTSLIB 1.9 for tabix/bgzip
42 RUN wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 && tar -xjvf htslib-1.9.tar.bz2 && \
43 cd htslib-1.9 && ./configure && make && make install
47 # Installing samtools 1.9
49 RUN wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 && tar -xjvf samtools-1.9.tar.bz2 && \
50 cd samtools-1.9 && ./configure && make && make install
54 # Installing bcftools 1.9
56 RUN wget https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2 && tar -xjvf bcftools-1.9.tar.bz2 && \
57 cd bcftools-1.9 && ./configure && make && make install