HiTE update to version 3.2

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit module / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# IDEA
+**/.idea/
+.idea
+/.idea/
+
+# demo
+demo/*

Dockerfile

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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
+
+# Download HiTE from Github
+# RUN git clone https://github.com/CSU-KangHu/HiTE.git
+
+# use local HiTE
+COPY HiTE-v.3.1.2.zip /HiTE-v.3.1.2.zip
+RUN cd / && unzip HiTE-v.3.1.2.zip && mv HiTE-v.3.1.2 /HiTE
+
+# Download HiTE from Zenodo
+#RUN curl -LJO https://zenodo.org/records/10574301/files/CSU-KangHu/HiTE-v.3.1.1.zip &&  \
+#    unzip HiTE-v.3.1.1.zip && mv CSU-KangHu-HiTE-* /HiTE
+
+RUN conda install mamba -c conda-forge -y
+RUN cd /HiTE && chmod +x tools/* && chmod +x bin/NeuralTE/tools/* && mamba env create --name ${DNAME} --file=environment.yml && conda clean -a
+
+# 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"]

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"]