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update dockerfile to download HiTE from zenodo
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@@ -2,26 +2,36 @@ FROM continuumio/miniconda3 | |
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# Author and maintainer | ||
MAINTAINER Kang Hu <[email protected]> | ||
LABEL description="HiTE: An accurate dynamic boundary adjustment approach for full-length Transposable Elements detection and annotation in Genome Assemblies" \ | ||
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]" | ||
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ARG DNAME="HiTE" | ||
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RUN apt-get update && apt-get install unzip --yes && apt-get install less --yes | ||
RUN apt-get update && apt-get install unzip --yes && apt-get install less --yes && apt-get install curl --yes | ||
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# Command 'RUN' during docker build | ||
#download RepeatMasker libraries | ||
RUN git clone https://github.com/CSU-KangHu/TE_annotation.git && \ | ||
cd TE_annotation && unzip RepeatMasker_Lib.zip | ||
#download RepeatMasker libraries from Github | ||
#RUN git clone https://github.com/CSU-KangHu/TE_annotation.git && \ | ||
# cd TE_annotation && unzip RepeatMasker_Lib.zip \ | ||
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# Download HiTE and create the environment | ||
#COPY environment.yml / | ||
RUN git clone https://github.com/CSU-KangHu/HiTE.git | ||
RUN cd /HiTE && conda env create --name ${DNAME} --file=environment.yml && conda clean -a | ||
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#update RepeatMasker libraries | ||
RUN mv /TE_annotation/RepeatMasker_Lib/* /opt/conda/envs/HiTE/share/RepeatMasker/Libraries/ | ||
#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 && cd CSU-KangHu-TE_annotation-* && unzip RepeatMasker_Lib.zip | ||
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# Download HiTE and create the environment | ||
# COPY environment.yml / | ||
# Download HiTE from Github | ||
# RUN git clone https://github.com/CSU-KangHu/HiTE.git | ||
# RUN cd /HiTE && conda env create --name ${DNAME} --file=environment.yml && conda clean -a | ||
# Download HiTE from Zenodo | ||
RUN curl -LJO https://zenodo.org/records/10065666/files/CSU-KangHu/HiTE-v.3.0.0.zip?download=1 && \ | ||
unzip HiTE-v.3.0.0.zip && cd CSU-KangHu-HiTE-* && chmod +x tools/* \ | ||
&& conda env create --name ${DNAME} --file=environment.yml && conda clean -a | ||
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# update RepeatMasker libraries from Github | ||
# RUN mv /TE_annotation/RepeatMasker_Lib/* /opt/conda/envs/HiTE/share/RepeatMasker/Libraries/ | ||
# update RepeatMasker libraries from Zenodo | ||
RUN mv /CSU-KangHu-TE_annotation-*/RepeatMasker_Lib/* /opt/conda/envs/HiTE/share/RepeatMasker/Libraries/ | ||
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# Make RUN commands use the new environment | ||
# name need to be the same with the above ${DNAME} | ||
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@@ -32,8 +42,12 @@ ENV PERL5LIB / | |
ENV PATH /opt/conda/envs/${DNAME}/bin:$PATH | ||
USER root | ||
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WORKDIR /HiTE | ||
# HiTE download from Github | ||
# WORKDIR /HiTE | ||
# RUN cd /HiTE | ||
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RUN cd /HiTE | ||
# HiTE download from Zenodo | ||
WORKDIR /CSU-KangHu-HiTE-* | ||
RUN cd /CSU-KangHu-HiTE-* | ||
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CMD ["bash"] |
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