From b9ffeed668fa9f90608731180189c97578c4ffff Mon Sep 17 00:00:00 2001
From: Gilquin <laurent.gilquin@ens-lyon.fr>
Date: Wed, 9 Nov 2022 11:54:21 +0100
Subject: [PATCH] modified installation steps

---
 README.md | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 519e0de..bc0ee6d 100644
--- a/README.md
+++ b/README.md
@@ -20,7 +20,7 @@ Conda is used to build the self-contained Python environnment that hosts the fol
 - **umap-learn** version **0.5.3**: used for building the umap embedding (instead of the default R package uwot),
 - **leidenalg** version **0.9.0 (or later)**: used for applying Leiden clustering algorithm when calling the `Seurat::FindClusters` function.
 
-Note that the conda environnment is only required for running one of the preprocessing scripts: `9396.R`, `WP.R` or `5hAPF.R`. Both the `test.R` and `analysis.R` scripts can be run without installing the conda environnment.
+Note that the conda environnment is only required for running one of the preprocessing scripts: `9396.R`, `WP.R` or `5hAPF.R`.
 
 ### Steps
 
@@ -28,7 +28,6 @@ Note that the conda environnment is only required for running one of the preproc
 2. Build the R environnment:
    * launch the R project `ClusteringAnalysis.Rproj`,
    * download the dependencies with the R command : `renv::restore()`
-3. (Optional) Create the conda environnment from the environnment file `seurat.yml`. See [this post](https://igfl.gitbiopages.ens-lyon.fr/websites/OldShack/python/r/2022/09/28/project-local-env.html#environment-file) for further instructions.
 
 ---
 
@@ -40,7 +39,7 @@ To perform the clustering analysis on the 9396, White Pupae or 5hAPF datasets :
 1. Create a folder named "data" at the project root and a subfolder of "results" where the figures and files will be stored,
 2. Copy the dataset in the "data" folder,
 3. Two options:
-   * either run the corresponding preprocessing script to build the ".h5Seurat" object (to do so, you need to have install the remote conda environnment),
+   * either run the corresponding preprocessing script to build the ".h5Seurat" object,
    * or, directly copy the corresponding ".h5Seurat" object in the "results" subfolder.
 4. Run the "analysis.R" with the following specifications:
    - the variable `savedir` should correctly point to the subfolder created at step 1,
-- 
GitLab