Dockerfile

FROM python:3.7

ENV talon_version=5.0
ENV bedtools_version=2.30.0
ENV TranscriptClean_version=2.0.3
ENV DEBIAN_FRONTEND=noninteractive

USER root

RUN apt-get update \
  && apt-get install --no-install-recommends -y build-essential wget unzip default-jre tabix procps libncurses5-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev zlib1g-dev libssl-dev gcc make perl bzip2 gnuplot ca-certificates gawk \
  && apt-get clean \
  && apt-get autoclean \
  && apt-get purge \
  && rm -rf /var/lib/apt/lists/* /tmp/*

RUN pip install --upgrade pip

WORKDIR /usr/local/

RUN wget https://github.com/mortazavilab/TALON/archive/refs/tags/v${talon_version}.zip \
  && wget https://github.com/arq5x/bedtools2/releases/download/v${bedtools_version}/bedtools-${bedtools_version}.tar.gz  \
  && wget https://github.com/mortazavilab/TranscriptClean/archive/refs/tags/v${TranscriptClean_version}.zip 

# unpack
RUN unzip v${talon_version}.zip \
  && tar -zxvf bedtools-${bedtools_version}.tar.gz \
  && unzip v${TranscriptClean_version}.zip 

WORKDIR /usr/local/TALON-${talon_version}
RUN pip install cython "setuptools<58.0.0" .

WORKDIR /usr/local/bedtools2
RUN make \
  && ln -s /usr/local/bedtools2/bin/bamToBed /usr/local/bin/bamToBed \
  && ln -s /usr/local/bedtools2/bin/bedtools /usr/local/bin/bedtools

RUN pip install pyfaidx pyranges pyfasta pandas

WORKDIR /usr/local/TranscriptClean-${TranscriptClean_version}
RUN cp -r ./* /usr/local/bin/
COPY ./bin/* /usr/local/bin/

WORKDIR /work