update dockerfile to download HiTE from zenodo

Dockerfile

@@ -2,26 +2,36 @@ FROM continuumio/miniconda3
 
 # 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]"
 
 ARG DNAME="HiTE"
 
-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
 
 # 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 \
 
-# 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
-
-#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
 
+# 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
+
+# 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/
 
 # Make RUN commands use the new environment
 # name need to be the same with the above ${DNAME}
@@ -32,8 +42,12 @@ ENV PERL5LIB /
 ENV PATH /opt/conda/envs/${DNAME}/bin:$PATH
 USER root
 
-WORKDIR /HiTE
+# HiTE download from Github
+# WORKDIR /HiTE
+# RUN cd /HiTE
 
-RUN cd /HiTE
+# HiTE download from Zenodo
+WORKDIR /CSU-KangHu-HiTE-*
+RUN cd /CSU-KangHu-HiTE-*
 
 CMD ["bash"]

README.md

@@ -43,12 +43,14 @@ Recommended OS: (Ubuntu 16.04, CentOS 7, etc.)
 ### Dowload project
 ```sh
 git clone https://github.com/CSU-KangHu/HiTE.git
+
+# Alternatively, you can download the zip file directly from the repository.
 ```
 
 ### <a name="install_singularity"></a>Option 1. Run with Singularity (recommended)
 ```sh
 # pull singularity image (once for all). There will be a HiTE.sif file.
-singularity pull HiTE.sif docker://kanghu/hite:2.0.4
+singularity pull HiTE.sif docker://kanghu/hite:3.0.0
 
 # run HiTE
 singularity run -B ${host_path}:${container_path} --pwd /HiTE ${pathTo/HiTE.sif} python main.py \
@@ -73,10 +75,10 @@ singularity run -B ${host_path}:${container_path} --pwd /HiTE ${pathTo/HiTE.sif}
 ### <a name="install_docker"></a>Option 2. Run with Docker
 ```sh
 # pull docker image (once for all).
-docker pull kanghu/hite:2.0.4
+docker pull kanghu/hite:3.0.0
 
 # run HiTE
-docker run -v ${host_path}:${container_path} kanghu/hite:2.0.4 python main.py \
+docker run -v ${host_path}:${container_path} kanghu/hite:3.0.0 python main.py \
  --genome ${genome} \
  --thread ${thread} \
  --outdir ${output_dir} \
@@ -87,7 +89,7 @@ docker run -v ${host_path}:${container_path} kanghu/hite:2.0.4 python main.py \
  #     It is recommended to set ${host_path} and ${container_path} to your user directory, and ensure 
  #     that all input and output files are located within the user directory.
 
- # e.g., my command: docker run -v /home/hukang:/home/hukang kanghu/hite:2.0.4 python main.py 
+ # e.g., my command: docker run -v /home/hukang:/home/hukang kanghu/hite:3.0.0 python main.py 
  # --genome /home/hukang/HiTE/demo/genome.fa 
  # --thread 40 
  # --outdir /home/hukang/HiTE/demo/test/