diff --git a/docker/reditools2/Dockerfile b/docker/reditools2/Dockerfile index 08f5071..fad8e6a 100644 --- a/docker/reditools2/Dockerfile +++ b/docker/reditools2/Dockerfile @@ -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 \"$@\"", "--"] CMD ["bash"] diff --git a/docker/reditools2/entrypoint.sh b/docker/reditools2/entrypoint.sh deleted file mode 100644 index 9d2850c..0000000 --- a/docker/reditools2/entrypoint.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash -source /opt/conda/etc/profile.d/conda.sh -conda activate myenv -exec "$@" diff --git a/singularity/reditools2/reditools2.def b/singularity/reditools2/reditools2.def index 84eb266..95bc809 100644 --- a/singularity/reditools2/reditools2.def +++ b/singularity/reditools2/reditools2.def @@ -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 @@ -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 @@ -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