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Fix Reditools2 on Singularity #33

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Merged
eascarrunz merged 2 commits into from
Jun 19, 2025
Merged

Fix Reditools2 on Singularity #33

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8e05b38
remove entrypoint script
eascarrunz Jun 19, 2025
39bbf20
fix def file for reditools2
eascarrunz Jun 19, 2025
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7 changes: 1 addition & 6 deletions docker/reditools2/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -6,17 +6,12 @@ RUN conda env create -n myenv --file env_reditools2.yml \
&& conda clean --all -f -y \
&& echo "conda activate myenv" >> ~/.bashrc # Auto-activating Conda setup for Python 2.7


# Get and install tools
RUN git clone --depth=1 https://github.com/BioinfoUNIBA/REDItools2.git reditools2
RUN chmod +x reditools2/src/cineca/reditools.py
RUN ln -n reditools2/src/cineca/reditools.py /usr/bin/reditools.py
RUN ln -n reditools2/src/cineca/parallel_reditools.py /usr/bin/parallel_reditools.py

# Set up Docker entrypoint for auto-activation of conda env
COPY entrypoint.sh /usr/local/bin/entrypoint.sh
RUN chmod +x /usr/local/bin/entrypoint.sh

ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
ENTRYPOINT ["/bin/bash", "-c", "source /opt/conda/etc/profile.d/conda.sh && conda activate myenv && exec \"$@\"", "--"]

CMD ["bash"]
4 changes: 0 additions & 4 deletions docker/reditools2/entrypoint.sh
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11 changes: 3 additions & 8 deletions singularity/reditools2/reditools2.def
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Expand Up @@ -3,7 +3,6 @@ From: condaforge/miniforge3:24.7.1-2

%files
singularity/reditools2/env_reditools2.yml ./env_reditools2.yml
singularity/reditools2/entrypoint.sh /usr/local/bin/entrypoint.sh

%post
# Activer conda dans l'environnement shell
Expand All @@ -12,7 +11,8 @@ From: condaforge/miniforge3:24.7.1-2

# Créer l'environnement Conda
conda create -n myenv python=2.7 -y
echo "conda activate myenv" >> /environment
echo "conda init" >> /root/.bashrc
echo "conda activate myenv" >> /root/.bashrc

# Mettre à jour avec le fichier YAML
conda env update -n myenv --file env_reditools2.yml
Expand All @@ -26,18 +26,13 @@ From: condaforge/miniforge3:24.7.1-2
ln -s /opt/reditools2/src/cineca/reditools.py /usr/local/bin/reditools.py
ln -s /opt/reditools2/src/cineca/parallel_reditools.py /usr/local/bin/parallel_reditools.py

# Entrypoint
chmod +x /usr/local/bin/entrypoint.sh

%environment
export PATH=/usr/local/bin:$PATH
export CONDA_DEFAULT_ENV=myenv
export PATH=/opt/conda/envs/myenv/bin:$PATH
source /opt/conda/etc/profile.d/conda.sh
conda activate myenv

%runscript
exec /usr/local/bin/entrypoint.sh "$@"
exec /bin/bash

%labels
Author jacques.dainat@ird.fr
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