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Improve installation instructions and improve env creation script #7

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7 changes: 7 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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

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4 changes: 2 additions & 2 deletions source_code/create_envs.sh
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@@ -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 .
Expand Down Expand Up @@ -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
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