1 # Copyright (C) The Lightning Authors. All rights reserved.
3 # SPDX-License-Identifier: AGPL-3.0
11 RUN apt-get install -qy build-essential wget cmake zlib1g-dev git
13 # Installing cgatools 1.8.0
15 RUN wget https://sourceforge.net/projects/cgatools/files/1.8.0/cgatools-1.8.0.1-linux_binary-x86_64.tar.gz && \
16 tar -xzvf cgatools-1.8.0.1-linux_binary-x86_64.tar.gz && \
17 cp cgatools-1.8.0.1-linux_binary-x86_64/bin/cgatools /usr/local/bin
21 # Getting HTSLIB for tabix/bgzip
23 RUN wget https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.bz2 && \
24 tar -xjvf htslib-1.3.1.tar.bz2 && \
25 cd htslib-1.3.1 && ./configure && make && make install
29 # Installing bedtools v2.25.0 and dependencies
31 RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz && \
32 tar -xzvf bedtools-2.25.0.tar.gz && \
33 cd bedtools2/ && make && cp /bedtools2/bin/bedtools /usr/local/bin
37 # Installing gvcf_regions
39 RUN git clone https://github.com/acoleman2000/gvcf_regions