From 1427b05aac6383fb23a373dad48c608ef79c4885 Mon Sep 17 00:00:00 2001
From: Jeroen Van Goey <j.vangoey@instadeep.com>
Date: Mon, 8 Sep 2025 15:27:02 +0200
Subject: [PATCH] improve installation instructions and fix env creation script

---
 README.md                  | 7 +++++++
 source_code/create_envs.sh | 4 ++--
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index dfdd56e..4f6c886 100644
--- a/README.md
+++ b/README.md
@@ -13,6 +13,13 @@ Run in command line
 ```
 git clone -b master https://github.com/SamvPy/DeNovo_Benchmark.git
 ```
+## Initialize git submodules
+
+Run in command line
+```
+git submodule update --init --recursive
+```
+
 
 ## Download conda
 
diff --git a/source_code/create_envs.sh b/source_code/create_envs.sh
index d3b8fbe..66c0c1f 100755
--- a/source_code/create_envs.sh
+++ b/source_code/create_envs.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # Install the denovo_utils package in its own environment
-cd ../package || exit
+cd ../package_du || exit
 conda env create -f denovo_analysis_env.yaml
 conda activate denovo_analysis_env
 pip install .
@@ -37,7 +37,7 @@ for env_dir in ./*; do
 
     # Activate the environment
     echo "Activating environment $env_name..."
-    source activate "${env_name,,}_env"
+    conda activate "${env_name,,}_env"
 
     # casanovo requires different installation procedure
     if [[ "$env_name" == "casanovo" ]]; then