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Dockerfile_3.0
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Dockerfile_3.0
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FROM continuumio/miniconda3
# Author and maintainer
MAINTAINER Kang Hu <[email protected]>
LABEL description="HiTE: A fast and accurate dynamic boundary adjustment approach for full-length Transposable Elements detection and annotation in Genome Assemblies" \
author="[email protected]"
ARG DNAME="HiTE"
RUN apt-get update && apt-get install unzip --yes && apt-get install less --yes && apt-get install curl --yes
# Command 'RUN' during docker build
# download RepeatMasker libraries from Github
# RUN git clone https://github.com/CSU-KangHu/TE_annotation.git && \
# cd TE_annotation && unzip RepeatMasker_Lib.zip \
# download RepeatMasker libraries from Zenodo
RUN curl -LJO https://zenodo.org/records/10068148/files/CSU-KangHu/TE_annotation-v3.0.zip?download=1 && \
unzip TE_annotation-v3.0.zip && mv CSU-KangHu-TE_annotation-* /TE_annotation && \
cd /TE_annotation && unzip RepeatMasker_Lib.zip
# Download HiTE from Github
# RUN git clone https://github.com/CSU-KangHu/HiTE.git
# Download HiTE from Zenodo
RUN curl -LJO https://zenodo.org/records/10158451/files/CSU-KangHu/HiTE-v.3.0.4.zip?download=1 && \
unzip HiTE-v.3.0.4.zip && mv CSU-KangHu-HiTE-* /HiTE
RUN cd /HiTE && chmod +x tools/* && conda env create --name ${DNAME} --file=environment.yml && conda clean -a
# update RepeatMasker libraries from Github
RUN mv /TE_annotation/RepeatMasker_Lib/* /opt/conda/envs/HiTE/share/RepeatMasker/Libraries/
# Make RUN commands use the new environment
# name need to be the same with the above ${DNAME}
SHELL ["conda", "run", "-n", "HiTE", "/bin/bash", "-c"]
# avoid different perl version conflict
ENV PERL5LIB /
ENV PATH /opt/conda/envs/${DNAME}/bin:$PATH
USER root
WORKDIR /HiTE
RUN cd /HiTE
CMD ["bash"]