HPGAP/DockerFile at master · vetscience/HPGAP · GitHub

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#!/usr/bin/bash
# Dockerfile
FROM ubuntu:16.04
RUN apt-get update && apt-get install -y wget bzip2 git
RUN apt-get install -y zip
RUN apt-get install -y unzip
RUN apt-get install -y vim
RUN apt-get install -y parallel
WORKDIR /root

LABEL about.license="BSD 3-clause License"
LABEL about.license_file="https://conda.io/docs/license.html"
LABEL about.license_file="https://repo.continuum.io/EULA/Anaconda+End+User+License+Agreement.txt"

RUN wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
RUN echo -e "\nyes\n" | bash Miniconda3-latest-Linux-x86_64.sh
ENV PATH=/root/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
RUN conda update -n base conda
RUN conda config --add channels defaults
RUN conda config --add channels conda-forge
RUN conda config --add channels bioconda
LABEL about.license_file=https://opensource.org/licenses/osl-2.1.php
RUN conda install samtools=1.9
RUN conda install bwa=0.7.8
RUN conda install bcftools=1.9
RUN conda install vcftools=0.1.16
RUN conda install plink=1.90b4
RUN conda install bbmap=38.22
RUN conda install snpeff=4.3k
RUN conda install picard=2.9.2
RUN conda install trimmomatic=0.38
LABEL about.license="BSD 3-Clause License"

RUN wget https://github.com/broadinstitute/gatk/releases/download/4.0.8.1/gatk-4.0.8.1.zip
RUN unzip gatk-4.0.8.1.zip
RUN ln -s gatk-4.0.8.1 gatk
ENV PATH=/root/gatk:/root/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
RUN apt-get install -y tabix
WORKDIR /root

RUN apt-get -y install r-base
#RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("ggplot2")'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("plyr")'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("reshape2")'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("gridExtra")'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("rmarkdown")'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("SNPRelate")'

RUN conda install pandoc=2.2.3.2
RUN conda install plink=1.90b4
RUN conda install beagle=4.1_21Jan17.6cc.jar
RUN conda install snpsift=4.3.1t

RUN wget http://www.genetics.ucla.edu/software/admixture/binaries/admixture_linux-1.3.0.tar.gz
RUN tar -xvf admixture_linux-1.3.0.tar.gz
ENV PATH=/root/admixture_linux-1.3.0/:/root/gatk:/root/miniconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

RUN snpEff download -c /root/miniconda3/share/snpeff-4.3k-0/snpEff.config -v Caenorhabditis_briggsae

RUN conda install -c bioconda phylip=3.697
RUN conda install -c bioconda treemix=1.12

RUN conda install -c anaconda numpy
RUN conda install -c bioconda pyvcf

RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("getopt")'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("phangorn")'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("gdsfmt")'

###Admixture
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("RColorBrewer")'

###For OrthoMCL
RUN conda create -n py27 python=2.7 anaconda
RUN conda install -n py27 numpy

###LD plot
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("dplyr")'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("stringr")'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("grid")'

RUN conda install -c bioconda muscle

#RUN /bin/bash -c 'source activate py27'

WORKDIR /root

###Dxy
COPY ./genomics_general /root/genomics_general

###Recalibration packages GATK
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("gplots")'
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("gsalib")'

RUN cpan YAML::Tiny
RUN conda install raxml=8.2.9
RUN conda install -c cswarth seqmagick=0.6.1

COPY ./jvarkit /root/jvarkit
WORKDIR /root/jvarkit
RUN make vcffilterjdk
WORKDIR /root

###MKtest
RUN conda install -c bioconda prank=v.170427
RUN cpan Bio::SeqIO
RUN cpan Text::NSP::Measures::2D::Fisher2::twotailed
RUN conda install -c bioconda dendropy=4.2.0

###SNPEff (only for testing)
ARG dbname="Clonorchis_sinensis_henan"
#ARG gff3="/home/darcy/PopGen_WorkFlow/Cs_Application/Input/SNPEFF/clonorchis_sinensis_henan.gff3"
#ARG fasta="/home/darcy/PopGen_WorkFlow/Cs_Application/Input/SNPEFF/Cs-c1.fa"
WORKDIR /root/miniconda3/share/snpeff-4.3k-0
RUN mkdir -p data/$dbname
COPY ./clonorchis_sinensis_henan.gff3 data/$dbname/genes.gff
COPY ./Cs-c1.fa data/$dbname/sequences.fa
RUN echo "$dbname.genome : $dbname" >> snpEff.config
RUN snpEff build -gff3 -v $dbname
WORKDIR /root/

RUN conda install -c conda-forge scikit-allel=1.2.0
RUN pip install tensorflow
RUN pip install keras
COPY ./diploSHIC /root/diploSHIC
WORKDIR /root/diploSHIC
RUN python setup.py install
WORKDIR /root/

COPY ./discoal /root/discoal/
WORKDIR /root/discoal
RUN make discoal
WORKDIR /root/

RUN conda install -c bioconda dadi=1.7.0
RUN pip install matplotlib

COPY ./LDhat /root/LDhat/
WORKDIR /root/LDhat/
RUN make

RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("seqGDS2VCF")'