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FROM ubuntu:18.04
LABEL base.image="ubuntu:18.04"
LABEL container.version="1.1.0"
LABEL software="iVar"
LABEL software.version="1.1-PR"
LABEL comments="Clone of ivar v1.1 pre-release most recent commit as of 05/09/2020"
LABEL description="Computational package that contains functions broadly useful for viral amplicon-based sequencing."
LABEL website="https://github.com/andersen-lab/ivar"
LABEL license="https://github.com/andersen-lab/ivar/blob/master/LICENSE"
LABEL maintainer="Kevin Libuit"
LABEL maintainer.email="kevin.libuit@dgs.virginia.gov"
LABEL modified.from="https://github.com/andersen-lab/ivar/blob/master/Dockerfile"
LABEL original.maintainer="Kathik G"
LABEL original.maintainer.email="gkarthik@scripps.edu"
RUN apt-get update
RUN apt-get install -y build-essential autoconf zlib1g-dev python3 wget libbz2-dev liblzma-dev libncurses-dev git bedtools python3-pip vim nano
# HTSlib
RUN cd root/ &&\
wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 &&\
tar xvf htslib-1.9.tar.bz2 &&\
cd htslib-1.9/ &&\
./configure &&\
make &&\
make install &&\
cd ../ &&\
rm htslib-1.9.tar.bz2
ENV LD_LIBRARY_PATH /usr/local/lib:$LD_LIBRARY_PATH
# SAMtools
RUN cd root &&\
wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 &&\
tar xvf samtools-1.9.tar.bz2 &&\
cd samtools-1.9/ &&\
./configure &&\
make &&\
make install &&\
cd ../ &&\
rm samtools-1.9.tar.bz2
# iVar v1.1-PR (most recent commit as of 03/19/2020)
RUN cd root/ &&\
git clone -n https://github.com/andersen-lab/ivar.git &&\
cd ivar/ &&\
git checkout 1610e0efee46459528a65769692936e1e35a17f3 &&\
./autogen.sh &&\
./configure &&\
make &&\
make install
# bwa
RUN mkdir bwa &&\
cd bwa &&\
wget https://github.com/lh3/bwa/archive/v0.7.17.tar.gz &&\
tar xvf v0.7.17.tar.gz &&\
rm v0.7.17.tar.gz &&\
cd bwa-0.7.17/ &&\
make
ENV PATH /root/bwa-0.7.17:$PATH
# Snakemake
RUN pip3 install pandas snakemake
# create /data directory and set as working directory
RUN mkdir /data
WORKDIR /data