From a87b547f802026c272bf0e5e1394de8a8d4c7ee3 Mon Sep 17 00:00:00 2001
From: Bonita van Waardenburg <bonita.vanwaardenburg@crg.eu>
Date: Fri, 19 Jun 2026 15:19:45 +0200
Subject: [PATCH] Updated fetch_submodules script

---
 fetch_submodules.sh | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/fetch_submodules.sh b/fetch_submodules.sh
index dbd0d51..152b18a 100644
--- a/fetch_submodules.sh
+++ b/fetch_submodules.sh
@@ -8,6 +8,7 @@ PAVIAN_ENV_DIR="$ENVS_DIR/pavian"
 
 mkdir -p "$BASE_DIR/submodules/10x_saturate"
 mkdir -p "$BASE_DIR/submodules/GeneExt"
+mkdir -p "$BASE_DIR/submodules/pavianCore"
 mkdir -p "$ENVS_DIR"
 
 echo "Fetching submodules..."
@@ -30,6 +31,14 @@ if [ ! -f "$BASE_DIR/submodules/GeneExt/environment.yaml" ]; then
     rm -rf /tmp/GeneExt-main /tmp/GeneExt.zip
 fi
 
+# PavianCore
+if [ ! -f "$BASE_DIR/submodules/pavianCore/exec/install_pavianCoreTools_packges.R" ]; then
+    echo "Downloading pavianCore..."
+    curl -L -o /tmp/pavianCore.zip https://github.com/Enthusiasm23/pavianCore/archive/refs/heads/master.zip
+    unzip -q /tmp/pavianCore.zip -d /tmp
+    cp -r /tmp/pavianCore-master/* "$BASE_DIR/submodules/pavianCore/"
+    rm -rf /tmp/pavianCore-master /tmp/pavianCore.zip
+
 echo "Submodules downloaded successfully!"
 
 echo "Setting up Pavian Conda environment..."