diff --git a/docs/source/install.md b/docs/source/install.md
index 90a8095485b0d3ba266bce8947f084d84d772f4c..bfb67f67de5350b12ba5ea87fb4caae25ddf6a20 100644
--- a/docs/source/install.md
+++ b/docs/source/install.md
@@ -12,7 +12,7 @@ $ git clone https://forgemia.inra.fr/umr-gdec/magatt.git
 We recommend to build the environment using conda (developped with miniconda 3, conda 4.9.2 ) with the file [environment.yml](https://forgemia.inra.fr/umr-gdec/magatt/-/blob/master/envs/environment.yml):  
 
 ```console
-$ conda env create -f environment.yml -n magatt
+$ conda env create -f envs/environment.yml -n magatt
 ```
 
 Once created, you can  activate the environment with:
diff --git a/docs/source/pipeline_conf.md b/docs/source/pipeline_conf.md
index e5feeb060985f6f570dd99d7f8475aa90a0d4a6f..ed5423a399361d3e1b4d2114a2a2af592c46de54 100644
--- a/docs/source/pipeline_conf.md
+++ b/docs/source/pipeline_conf.md
@@ -31,7 +31,7 @@ Here, we only need the fasta of the new genome assembly
 | Parameter in `config.yaml` | format |description |Example |  
 |----------------------------|--------|------------|--------|  
 |**targetFasta**|FASTA|fasta file of the target genome assembly on which we transfert the annotation|targetFasta: 'data/CS_pesudo_v2.1.fa'|  
-|**targetBwaIdx**|BWA index|Prefix for the BWA index files|targetBwaIdx: '/data/db/triticum_aestivum/arinalrfor/current/bwa/all'|  
+|**targetBwaIdx**|BWA index|Prefix for the BWA index files|targetBwaIdx: '/data/db/triticum_aestivum/julius/current/bwa/all'|  
 |**targetGmapIndex**|PATH|Name of the GMAP index directory. This will be used with the `-d` option of `gmapl`|targetGmapIndex: 'ensembl_Triticum_aestivum_julius_2022-9-16'|  
 |**targetGmapIndexPath**|PATH|Full path to the directory in which the GMAPindex is found. This will be used with the `-D` option of `gmapl`|targetGmapIndexPath: '/data/db/triticum_aestivum/julius/gmapdb/all/'|  
 
diff --git a/docs/source/run_pipeline.md b/docs/source/run_pipeline.md
index 5e54a68da8c12b9c6ca890f117e9de9318d2e93f..f355363706f93da8575e040295ec9cad49cac427 100644
--- a/docs/source/run_pipeline.md
+++ b/docs/source/run_pipeline.md
@@ -32,7 +32,7 @@ $ snakemake -j 32 --cluster sbatch
 
 This will allow to have at most 32 subproccess run through the SLURM scheduler with `sbatch`.
 
-You can use a custom [cluster.json](https://forgemia.inra.fr/umr-gdec/magatt/-/blob/master/cluster.json) JSON file do setup the parameters of SBATCH for each rules, and use it with with:    
+You can use a custom [cluster.json](https://forgemia.inra.fr/umr-gdec/magatt/-/blob/master/cluster-hpc2.json) JSON file do setup the parameters of SBATCH for each rules, and use it with with:    
 
 ```console
 $ snakemake -j 32 --cluster-config cluster-hpc2.json --cluster "sbatch -J {cluster.jobName} -c {cluster.c} --mem {cluster.mem} -e {cluster.error} -o {cluster.output} -p gdec" --verbose"