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notebooks/Snakemake/AWS-ParallelCluster.ipynb

@@ -170,7 +170,7 @@
    "id": "73692fbe",
    "metadata": {},
    "source": [
-    "3. Install conda. This is required as we will be executing Snakemake using conda. "
+    "3. Install mamba. This is required as we will be executing Snakemake using mamba. "
    ]
   },
   {
@@ -179,12 +179,10 @@
    "metadata": {},
    "source": [
     "```bash\n",
-    "wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh\n",
-    "bash ~/miniconda.sh\n",
-    "~/miniconda3/bin/conda init\n",
-    "source ~/.bashrc\n",
-    "which conda\n",
-    "conda --version\n",
+    "wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\n",
+    "bash Miniconda3-latest-Linux-x86_64.sh\n",
+    "conda install mamba -c conda-forge\n",
+    "mamba --version\n",
     "```"
    ]
   },
@@ -718,13 +716,13 @@
     "Execute the workflow using the **Snakemake** command, specifying **pcluster-Slurm** as the executor and **conda** as the environment management system\n",
     "\n",
     "```bash\n",
-    "Snakemake --executor pcluster-Slurm --use-conda -j 5\n",
+    "Snakemake --executor pcluster-Slurm --use-conda --conda-frontend mamba -j 5\n",
     "```\n",
     "#### Commandline Command Breakdown: \n",
     "\n",
-    "**--use-conda** \n",
+    "**--use-conda --conda-frontend mamba** \n",
     "\n",
-    "This flag tells Snakemake to use Conda environments for managing dependencies. When this flag is used, Snakemake will look for environment.yaml files specified in the workflow rules and create Conda environments accordingly. \n",
+    "This flag tells Snakemake to use mamba environments for managing dependencies. When this flag is used, Snakemake will look for environment.yaml files specified in the workflow rules and create mamba environments accordingly. \n",
     "\n",
     "**-j** \n",
     "\n",
@@ -769,7 +767,11 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 5
 }