From 8e05b387926ba70ddbd8a8b61577e9d43b72a686 Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 19 Jun 2025 15:52:29 +0200
Subject: [PATCH 1/2] remove entrypoint script

---
 docker/reditools2/Dockerfile    | 7 +------
 docker/reditools2/entrypoint.sh | 4 ----
 2 files changed, 1 insertion(+), 10 deletions(-)
 delete mode 100644 docker/reditools2/entrypoint.sh

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 "$@"

From 39bbf20c6e079fe105682c5c86e034a82c53987a Mon Sep 17 00:00:00 2001
From: earx <eascarrunz.dev@mailfence.com>
Date: Thu, 19 Jun 2025 16:17:17 +0200
Subject: [PATCH 2/2] fix def file for reditools2

---
 singularity/reditools2/reditools2.def | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

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