Merge pull request #3 from NIGMS/migration_to_batch

Migration to batch

Author: kyleoconnell-NIH

Submodule_00_background.ipynb

@@ -405,9 +405,9 @@
  "metadata": {
   "environment": {
    "kernel": "python3",
-   "name": "common-cpu.m108",
+   "name": "common-cpu.m109",
    "type": "gcloud",
-   "uri": "gcr.io/deeplearning-platform-release/base-cpu:m108"
+   "uri": "gcr.io/deeplearning-platform-release/base-cpu:m109"
   },
   "kernelspec": {
    "display_name": "Python 3",
@@ -424,7 +424,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.12"
+   "version": "3.10.11"
   }
  },
  "nbformat": 4,

Submodule_01_prog_setup.ipynb

@@ -305,7 +305,7 @@
    "outputs": [],
    "source": [
     "from jupyterquiz import display_quiz\n",
-    "display_quiz(\"rnaAssemblyMDI/quiz-material/01-cp1.json\", shuffle_questions = True)"
+    "display_quiz(\"Transcriptome-Assembly-Refinement-and-Applications/quiz-material/01-cp1.json\", shuffle_questions = True)"
    ]
   },
   {
@@ -315,14 +315,22 @@
    "source": [
     "## When you are ready, proceed to the next notebook: [`Submodule_02_basic_assembly.ipynb`](./Submodule_02_basic_assembly.ipynb)."
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "934165c2-8fbd-4801-979f-6db5d1e592ea",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
   "environment": {
    "kernel": "python3",
-   "name": "common-cpu.m104",
+   "name": "common-cpu.m109",
    "type": "gcloud",
-   "uri": "gcr.io/deeplearning-platform-release/base-cpu:m104"
+   "uri": "gcr.io/deeplearning-platform-release/base-cpu:m109"
   },
   "kernelspec": {
    "display_name": "Python 3",
@@ -339,7 +347,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.12"
+   "version": "3.10.11"
   }
  },
  "nbformat": 4,

Submodule_02_basic_assembly.ipynb

@@ -275,8 +275,8 @@
    "outputs": [],
    "source": [
     "from jupytercards import display_flashcards\n",
-    "display_flashcards('rnaAssemblyMDI/quiz-material/02-cp1-1.json')\n",
-    "display_flashcards('rnaAssemblyMDI/quiz-material/02-cp1-2.json')"
+    "display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/02-cp1-1.json')\n",
+    "display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/02-cp1-2.json')"
    ]
   },
   {
@@ -291,9 +291,9 @@
  "metadata": {
   "environment": {
    "kernel": "python3",
-   "name": "common-cpu.m104",
+   "name": "common-cpu.m109",
    "type": "gcloud",
-   "uri": "gcr.io/deeplearning-platform-release/base-cpu:m104"
+   "uri": "gcr.io/deeplearning-platform-release/base-cpu:m109"
   },
   "kernelspec": {
    "display_name": "Python 3",
@@ -310,7 +310,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.12"
+   "version": "3.10.11"
   }
  },
  "nbformat": 4,

Submodule_03_annotation_only.ipynb

@@ -308,6 +308,18 @@
     "YouTubeVideo('D95mFnIjRo4', width=800, height=400)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "82296cfb-cddb-4325-a8a6-ab3eea8fdfbd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "numthreads=!lscpu | grep '^CPU(s)'| awk '{print $2-1}'\n",
+    "THREADS = int(numthreads[0])\n",
+    "!echo $THREADS"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -318,7 +330,7 @@
     "!docker run -it --rm --volume /home:/home quay.io/biocontainers/busco:5.4.3--pyhdfd78af_0 busco \\\n",
     "-i /home/jupyter/resources/trans/Oncorhynchus_mykiss_GGBN01.1.fa \\\n",
     "-l vertebrata_odb10 -o GGBN01_busco_vertebrata \\\n",
-    "--out_path /home/jupyter/buscoOutput -m tran -c 14 "
+    "--out_path /home/jupyter/buscoOutput -m tran -c $THREADS"
    ]
   },
   {
@@ -365,7 +377,7 @@
    "outputs": [],
    "source": [
     "from jupytercards import display_flashcards\n",
-    "display_flashcards('rnaAssemblyMDI/quiz-material/03-cp1-1.json')"
+    "display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/03-cp1-1.json')"
    ]
   },
   {
@@ -385,7 +397,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "display_flashcards('rnaAssemblyMDI/quiz-material/03-cp1-2.json')"
+    "display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/03-cp1-2.json')"
    ]
   },
   {
@@ -415,7 +427,7 @@
     "!docker run -it --rm --volume /home:/home quay.io/biocontainers/busco:5.4.3--pyhdfd78af_0 busco \\\n",
     "-i /home/jupyter/resources/trans/Pseudacris_regilla_GAEI01.1.fa \\\n",
     "-l vertebrata_odb10 -o GAEI01_busco_vertebrata \\\n",
-    "--out_path /home/jupyter/buscoOutput -m tran -c 14 "
+    "--out_path /home/jupyter/buscoOutput -m tran -c $THREADS"
    ]
   },
   {
@@ -473,9 +485,9 @@
  "metadata": {
   "environment": {
    "kernel": "python3",
-   "name": "common-cpu.m108",
+   "name": "common-cpu.m109",
    "type": "gcloud",
-   "uri": "gcr.io/deeplearning-platform-release/base-cpu:m108"
+   "uri": "gcr.io/deeplearning-platform-release/base-cpu:m109"
   },
   "kernelspec": {
    "display_name": "Python 3",
@@ -492,7 +504,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.12"
+   "version": "3.10.11"
   }
  },
  "nbformat": 4,