diff --git a/custom_install.sh b/custom_install.sh
index f2a87f1..a22bcb0 100644
--- a/custom_install.sh
+++ b/custom_install.sh
@@ -4,10 +4,12 @@
 # cd serum_readfilter
 # pip install .
 
-#ENV_NAME=$1
+ENV_NAME=$1
+echo "Environment $ENV_NAME and $1"
+
 
 GIT_REPO=https://github.com/ssi-dk/serum_readfilter
-REPO_FOLDER=serum_readfilter
+REPO_FOLDER="serum_readfilter"
 SUBMODULE_PATH="bifrost_sp_cdiff/cdiff_fbi"  # Path to the submodule
 
 SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
@@ -19,51 +21,61 @@ function exit_function() {
   exit 1
 }
 
-CONDA_BASE=$(conda info --base)
-source $CONDA_BASE/etc/profile.d/conda.sh
 
-# if ! (conda env list | grep "$ENV_NAME")
-# then
+#CONDA_BASE=$(conda info --base)
+#source $CONDA_BASE/etc/profile.d/conda.sh
+#conda env list | grep "$ENV_NAME"
+
+#if ! (conda env list | grep "$ENV_NAME")
+#then
 #   echo "Conda environment specified is not found"
 #   exit_function
-# else
+#else
 #   conda activate $ENV_NAME
-# fi
+#fi
+#echo "packages before activating the environment"
+#which python
+#which pip
+
+#echo "before activate environmment"
+#conda info
+#echo "activate conda environment $ENV_NAME"
+#conda activate $ENV_NAME
+#ls /home/projects/fvst_ssi_dtu/apps/sofi_bifrost_dev/conda/envs/
+#ls /home/projects/fvst_ssi_dtu/apps/sofi_bifrost_dev/conda/envs/bifrost_dev_sp_cdiff_v0.0.1/
+echo "Activating conda environment $ENV_NAME"
+
+# Ensure conda is properly sourced
+CONDA_BASE=$(conda info --base)
+source $CONDA_BASE/etc/profile.d/conda.sh
 
-if test -d "$SCRIPT_DIR/$REPO_FOLDER"
-then
-  echo "$SCRIPT_DIR/$REPO_FOLDER already exists, if you want to overwrite, please remove the old repository folder"
-  echo "You can use:"
-  echo "rm -rf $SCRIPT_DIR/$REPO_FOLDER"
+# Check if the environment exists
+if ! conda env list | grep -q "$ENV_NAME"; then
+    echo "Conda environment $ENV_NAME does not exist. Please ensure it is created."
+    exit 1
+fi
+
+CONDA_ENV_PATH=$(conda env list|awk '{print $2}' | grep -v '^$'|grep "$ENV_NAME")
+
+conda activate $ENV_NAME
+
+git clone $GIT_REPO
+cd $REPO_FOLDER
+echo "#################Installing package using pip"
+PIP_PATH="$CONDA_ENV_PATH/bin/pip"
+echo "installed pip path $INSTALLED_PIP_PATH"
+$PIP_PATH install .
+# Check where serum_readfilter is installed
+INSTALLED_PATH=$(which serum_readfilter)
+
+if [[ "$INSTALLED_PATH" == "~/.local/bin/serum_readfilter" ]]; then
+  echo "Warning: serum_readfilter is installed in ~/.local/bin, which may cause conflicts."
   exit_function
-else
-  git --version
-  GIT_IS_AVAILABLE=$?
-  if [ $GIT_IS_AVAILABLE -eq 0 ]
-  then
-    echo "#################Cloning repository from $GIT_REPO"
-    if ! git clone $GIT_REPO
-    then
-      echo >&2 "git clone command failed"
-      exit_function
-    else
-      cd $REPO_FOLDER
-      echo "#################Installing package using pip"
-      if ! pip install .
-      then
-        echo >&2 "pip install command failed"
-        exit_function
-      else
-        echo "Package successfully installed"
-      fi
-    fi
-  else
-    echo "git is not installed"
-    echo "You can try installing git and rerunning the script"
-    exit_function
-  fi
 fi
 
+echo "serum_readfilter is installed at: $INSTALLED_PATH"
+conda deactivate
+
 cd $SCRIPT_DIR
 
 # Initialize and update submodules
@@ -75,7 +87,6 @@ fi
 
 cd $SUBMODULE_PATH || { echo "Failed to enter submodule cdiff_fbi repository directory"; exit_function; }
 
-
 # Fetch the latest tags
 echo "################# Fetching the latest tags for the submodule..."
 if ! git fetch origin --tags; then
diff --git a/install.sh b/install.sh
index dfc4787..335b4be 100644
--- a/install.sh
+++ b/install.sh
@@ -159,6 +159,7 @@ fi
 #check if custom_install.sh file exists and run it
 if test -f "$CUSTOM_INSTALL_PATH";
 then
-  echo -e "\nRunning custom_install.sh"
+  echo -e "\nRunning custom_install.sh -> bash -i $CUSTOM_INSTALL_PATH $ENV_NAME"
   bash -i $CUSTOM_INSTALL_PATH $ENV_NAME #-i required for interactive mode to active env
+  #bash $CUSTOM_INSTALL_PATH $ENV_NAME
 fi