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Dockerfile
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Dockerfile
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# syntax=docker/dockerfile:1
FROM ubuntu:latest
WORKDIR /project
ENV DEBIAN_FRONTEND=noninteractive \
TZ=America/New_York
RUN apt-get update && apt-get install -y \
bcftools \
git \
tzdata \
python3 \
python3-pip \
raxml \
seqtk \
samtools \
seaview \
wget \
&& apt-get -y autoremove \
&& apt-get clean autoclean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
#install python and symlink python3 to python
#RUN apt-get install -y python3
#RUN apt-get install -y python3-pip
RUN ln -s /usr/bin/python3 /usr/bin/python
RUN pip3 install dendropy --no-cache-dir
#install dependencies available from apt-get
#RUN apt-get install raxml
#RUN apt-get install seqtk
#RUN apt-get install bcftools -y
#RUN apt-get install samtools -y
#RUN apt-get install git -y
#RUN apt-get install seaview -y
#fastx toolkit and bwa-mem need wget to be installed
#RUN apt-get install wget -y
RUN wget http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2 \
&& tar -xjf fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2 \
&& cp bin/* /usr/local/bin/ \
&& rm -rf bin fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2
#RUN tar -xjf fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2
#RUN cp ./bin/* /usr/local/bin/
RUN wget https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2/bwa-mem2-2.0pre2_x64-linux.tar.bz2 \
&& tar -xjf bwa-mem2-2.0pre2_x64-linux.tar.bz2 \
&& cp ./bwa-mem2-2.0pre2_x64-linux/bwa-mem2* /usr/local/bin/ \
&& rm -rf bwa-mem2-2.0pre2_x64-linux.tar.bz2 bwa-mem2-2.0pre2_x64-linux
#RUN tar -xjf bwa-mem2-2.0pre2_x64-linux.tar.bz2
#RUN cp ./bwa-mem2-2.0pre2_x64-linux/bwa-mem2* /usr/local/bin/
# install Extensiphy
RUN git clone https://github.com/McTavishLab/extensiphy.git
WORKDIR /project/extensiphy