Try %%bash

Author: tomwhite

docs/examples/gwas_tutorial.ipynb

@@ -101,23 +101,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
-   "id": "69cddb00-63fa-4dbc-8d50-5a5859e1c42d",
+   "execution_count": 6,
+   "id": "78effc1d-b45e-4af5-85ae-e0e7a40ca049",
    "metadata": {},
    "outputs": [
     {
-     "name": "stdout",
+     "name": "stderr",
      "output_type": "stream",
      "text": [
-      "    Scan:   0%|                                  | 0.00/1.00 [00:00<?, ?files/s][W::bcf_hdr_check_sanity] PL should be declared as Number=G\n",
-      "    Scan: 100%|███████████████████████████| 1.00/1.00 [00:01<00:00, 1.00s/files]\n",
-      " Explode:   0%|                                  | 0.00/10.9k [00:00<?, ?vars/s][W::bcf_hdr_check_sanity] PL should be declared as Number=G\n",
-      " Explode: 100%|███████████████████████████| 10.9k/10.9k [00:19<00:00, 548vars/s]\n"
+      "    Scan:   0%|          | 0.00/1.00 [00:00<?, ?files/s][W::bcf_hdr_check_sanity] PL should be declared as Number=G\n",
+      "    Scan: 100%|██████████| 1.00/1.00 [00:00<00:00, 1.05files/s]\n",
+      " Explode:   0%|          | 0.00/10.9k [00:00<?, ?vars/s][W::bcf_hdr_check_sanity] PL should be declared as Number=G\n",
+      " Explode: 100%|██████████| 10.9k/10.9k [00:20<00:00, 541vars/s]\n"
      ]
     }
    ],
    "source": [
-    "! vcf2zarr explode --force 1kg.vcf.bgz 1kg.icf"
+    "%%bash\n",
+    "vcf2zarr explode --force 1kg.vcf.bgz 1kg.icf"
    ]
   },
   {