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FROM ubuntu:18.04
MAINTAINER Karthik G <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:$LD_LIBRARY_PATH
# SAMtools
RUN cd root &&\
wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 &&\
tar xvf samtools-1.9.tar.bz2 &&\
cd samtools-1.9/ &&\
./configure &&\
make &&\
make install &&\
cd ../ &&\
rm samtools-1.9.tar.bz2
# iVar
RUN cd root/ &&\
git clone https://github.com/andersen-lab/ivar.git &&\
cd ivar/ &&\
./autogen.sh &&\
./configure &&\
make &&\
make install
# bwa
RUN cd root/ &&\
wget https://github.com/lh3/bwa/archive/v0.7.17.tar.gz &&\
tar xvf v0.7.17.tar.gz &&\
cd bwa-0.7.17/ &&\
make &&\
cd ../ &&\
rm v0.7.17.tar.gz
ENV PATH /root/bwa-0.7.17:$PATH
# Snakemake
RUN pip3 install pandas snakemake