Merged changes

Author: alancleary

module_notebooks/01-intro-to-pangenomics.ipynb

@@ -238,32 +238,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "\n",
-       "        <iframe\n",
-       "            width=\"800\"\n",
-       "            height=\"400\"\n",
-       "            src=\"../html/quiz_pangenomes.html\"\n",
-       "            frameborder=\"0\"\n",
-       "            allowfullscreen\n",
-       "            \n",
-       "        ></iframe>\n",
-       "        "
-      ],
-      "text/plain": [
-       "<IPython.lib.display.IFrame at 0x7f2dee2f42f0>"
-      ]
-     },
-     "execution_count": 1,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "from IPython.display import IFrame\n",
     "IFrame('../html/quiz_pangenomes.html', width=800, height=400)"
@@ -292,12 +269,6 @@
   }
  ],
  "metadata": {
-  "environment": {
-   "kernel": "conda-env-nigms-pangenomics-nigms-pangenomics",
-   "name": "workbench-notebooks.m129",
-   "type": "gcloud",
-   "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m129"
-  },
   "kernelspec": {
    "display_name": "nigms-pangenomics (Local)",
    "language": "python",

module_notebooks/02-building-graphs-with-pggb.ipynb

@@ -1124,19 +1124,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 28,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "sed: -e expression #1, char 17: unknown command: `o'\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
-    "!sed -n '/pggb -i graphs/output_allchrs/,$p' graphs/output_allchrs/*.log > graphs/run-pggb-partitions.sh\n",
+    "!sed -n '/pggb -i graphs\\/output_allchrs/,$p' graphs/output_allchrs/*.log > graphs/run-pggb-partitions.sh\n",
     "!chmod +x graphs/run-pggb-partitions.sh"
    ]
   },
@@ -1156,7 +1148,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 29,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1325,7 +1317,7 @@
    "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m129"
   },
   "kernelspec": {
-   "display_name": "nigms-pangenomics (Local) (Local)",
+   "display_name": "nigms-pangenomics (Local)",
    "language": "python",
    "name": "conda-env-nigms-pangenomics-nigms-pangenomics"
   },