1 # Copyright (C) The Lightning Authors. All rights reserved.
3 # SPDX-License-Identifier: AGPL-3.0
6 MAINTAINER Jiayong Li <jli@curii.com>
12 RUN apt-get install -qy build-essential wget cmake zlib1g-dev \
13 libbz2-dev liblzma-dev libncurses5-dev libncursesw5-dev git vcftools
15 # Getting HTSLIB 1.9 for tabix/bgzip
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
22 # Installing samtools 1.9
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
29 # Installing bcftools 1.9
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
36 # Installing rtg tools v3.8.4
38 RUN apt-get install -qy unzip
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
44 ENV PATH="/rtg-tools-3.9.1:${PATH}"
48 # Installing bedops v2.4.35
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
56 # Installing bedtools 2.27.1
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
64 # Installing gvcf_regions
66 RUN git clone https://github.com/lijiayong/gvcf_regions