Add a python3.12.6 venv to the R and FCPS apptainers

Author: imallona

envs/clustbench_singularity.def

@@ -33,6 +33,3 @@ From: ubuntu:jammy-20240911.1
 %environment
 
     . /opt/default/bin/activate
-    echo $PATH
-    python --version
-    python3.12 --version

envs/fcps_singularity.def

@@ -7,15 +7,29 @@ From: rocker/tidyverse:4.4
 
 %post
 
-    # Install python packages
-
+    # Install python3.12
     apt-get update
-    apt-get -y install python3 python3-pip python3-dev python-is-python3 git
-    
-    pip3 install -U argparse gitpython isodate pydantic-core 
+    apt install -y build-essential zlib1g-dev libncurses5-dev libgdbm-dev libnss3-dev libssl-dev \
+        libreadline-dev libffi-dev libsqlite3-dev wget libbz2-dev python-is-python3 git
+
+    wget https://www.python.org/ftp/python/3.12.6/Python-3.12.6.tgz
+    tar -xf Python-3.12.6.tgz
+    cd Python-3.12.*/
+    ./configure --enable-optimizations
+    make -j 4
+    make altinstall
 
-    # Install R packages
+    # virtualenv
+    cd /opt
+    python3.12 -m venv "default"
+    . default/bin/activate
+
+    pip install gitpython==3.1.43 isodate pydantic-core
 
-    Rscript -e 'BiocManager::install(c("fcps", "dbscan", "protoclust", "energy", "argparse"))'
+    Rscript -e 'BiocManager::install(c("FCPS", "dbscan", "protoclust", "energy", "argparse"))'
+
+    echo '. /opt/default/bin/activate' >> $SINGULARITY_ENVIRONMENT
 
 %environment
+    
+    . /opt/default/bin/activate

envs/r_singularity.def

@@ -7,17 +7,31 @@ From: rocker/tidyverse:4.4
 
 %post
 
-    # Install python packages
-
+    # Install python3.12
     apt-get update
-    apt-get -y install python3 python3-pip python3-dev python-is-python3 git
-    
-    pip3 install argparse gitpython isodate pydantic-core
+    apt install -y build-essential zlib1g-dev libncurses5-dev libgdbm-dev libnss3-dev libssl-dev \
+        libreadline-dev libffi-dev libsqlite3-dev wget libbz2-dev python-is-python3 git
+
+    wget https://www.python.org/ftp/python/3.12.6/Python-3.12.6.tgz
+    tar -xf Python-3.12.6.tgz
+    cd Python-3.12.*/
+    ./configure --enable-optimizations
+    make -j 4
+    make altinstall
+
+    # virtualenv
+    cd /opt
+    python3.12 -m venv "default"
+    . default/bin/activate
+
+    pip install gitpython==3.1.43 isodate pydantic-core
 
-    #################################
     # Install R packages
-    #################################
 
     Rscript -e 'BiocManager::install(c("mclust", "caret", "readr", "argparse"))'
 
+    echo '. /opt/default/bin/activate' >> $SINGULARITY_ENVIRONMENT
+
 %environment
+
+    . /opt/default/bin/activate