Merge pull request #15 from montgomerymt-NIH/main

Fundamentals of Bioinformatics GCP update
NIGMS · Nov 21, 2024 · 45fce70 · 45fce70
2 parents 1d523ea + 5ea50c1
commit 45fce70
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diff --git a/GoogleCloud/submodule01_Intro_to_terminal.ipynb b/GoogleCloud/submodule01_Intro_to_terminal.ipynb
@@ -106,7 +106,7 @@
     "# FLASHCARDS\n",
     "\n",
     "from IPython.display import IFrame\n",
-    "IFrame(\"quiz_files/quiz1-1.html\", width=600, height=250)"
+    "IFrame(\"quiz_files/quiz1-1.html\", width=600, height=350)"
    ]
   },
   {
@@ -462,7 +462,7 @@
    "source": [
     "#FLASHCARD\n",
     "from IPython.display import IFrame\n",
-    "IFrame(\"quiz_files/quiz1-2.html\", width=600, height=250)"
+    "IFrame(\"quiz_files/quiz1-2.html\", width=600, height=350)"
    ]
   },
   {
@@ -505,7 +505,7 @@
    "source": [
     "# FLASHCARD\n",
     "from IPython.display import IFrame\n",
-    "IFrame(\"quiz_files/quiz1-3.html\", width=600, height=250)"
+    "IFrame(\"quiz_files/quiz1-3.html\", width=600, height=350)"
    ]
   },
   {

diff --git a/GoogleCloud/submodule03_genomics_file_format.ipynb b/GoogleCloud/submodule03_genomics_file_format.ipynb
@@ -639,7 +639,7 @@
    "source": [
     "# FLASHCARD\n",
     "from IPython.display import IFrame\n",
-    "IFrame(\"quiz_files/quiz3-1.html\", width=600, height=250)"
+    "IFrame(\"quiz_files/quiz3-1.html\", width=600, height=350)"
    ]
   },
   {
@@ -766,7 +766,7 @@
     "\n",
     "# Step 1\n",
     "# Print the first 10,000 reads\n",
-    "zcat gcp_research_workflow/SRR1039508_1.chr20.fastq.gz | sed -n '2~4p' | head -n 10000 "
+    "zcat gcp_research_workflow/SRR1039508_1.chr20.fastq.gz | sed -n '2~4p' | head -n 100 "
    ]
   },
   {
@@ -780,7 +780,7 @@
     "\n",
     "# Step 2\n",
     "# Print each base from the first 10,000 reads to it's own line\n",
-    "zcat gcp_research_workflow/SRR1039508_1.chr20.fastq.gz | sed -n '2~4p' | head -n 10000 | grep -o . "
+    "zcat gcp_research_workflow/SRR1039508_1.chr20.fastq.gz | sed -n '2~4p' | head -n 100 | grep -o . "
    ]
   },
   {
@@ -794,7 +794,7 @@
     "\n",
     "# Step 3\n",
     "# Sort the bases from the first 10,000 reads\n",
-    "zcat gcp_research_workflow/SRR1039508_1.chr20.fastq.gz | sed -n '2~4p' | head -n 10000 | grep -o . | sort "
+    "zcat gcp_research_workflow/SRR1039508_1.chr20.fastq.gz | sed -n '2~4p' | head -n 100 | grep -o . | sort "
    ]
   },
   {
@@ -808,7 +808,7 @@
     "\n",
     "# Step 4\n",
     "# Isolate the \"N\" bases from the first 10,000 reads\n",
-    "zcat gcp_research_workflow/SRR1039508_1.chr20.fastq.gz | sed -n '2~4p' | head -n 10000 | grep -o . | sort | grep 'N' "
+    "zcat gcp_research_workflow/SRR1039508_1.chr20.fastq.gz | sed -n '2~4p' | head -n 100 | grep -o . | sort | grep 'N' "
    ]
   },
   {
@@ -880,7 +880,7 @@
    "source": [
     "# FLASHCARD\n",
     "from IPython.display import IFrame\n",
-    "IFrame(\"quiz_files/quiz3-2.html\", width=600, height=250)"
+    "IFrame(\"quiz_files/quiz3-2.html\", width=600, height=350)"
    ]
   },
   {

diff --git a/GoogleCloud/submodule04_beyond_basic_bash.ipynb b/GoogleCloud/submodule04_beyond_basic_bash.ipynb
@@ -172,7 +172,7 @@
    "source": [
     "# FLASHCARD\n",
     "from IPython.display import IFrame\n",
-    "IFrame(\"quiz_files/quiz4-1.html\", width=600, height=250)"
+    "IFrame(\"quiz_files/quiz4-1.html\", width=600, height=350)"
    ]
   },
   {
@@ -433,7 +433,7 @@
    "source": [
     "# FLASHCARD\n",
     "from IPython.display import IFrame\n",
-    "IFrame(\"quiz_files/quiz4-2.html\", width=600, height=250)"
+    "IFrame(\"quiz_files/quiz4-2.html\", width=600, height=350)"
    ]
   },
   {

diff --git a/GoogleCloud/submodule05_software_management.ipynb b/GoogleCloud/submodule05_software_management.ipynb
@@ -88,7 +88,7 @@
    "id": "f712d9a8-c807-43ee-b486-27dc01b7d088",
    "metadata": {},
    "source": [
-    "cd into the directory outputed from the command above."
+    "cd into the directory outputed from the command above. Open the terminal, type `cd`, then press [Enter]."
    ]
   },
   {
@@ -145,7 +145,19 @@
    "id": "ebfc4dad-2c75-49c0-99aa-459a730d3209",
    "metadata": {},
    "source": [
-    "Run the following command to jump start the process."
+    "Run the following commands to jump start the process."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "46d5fd0a-ed71-4fbf-82fa-0d40cbb3533a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%bash\n",
+    "# Install nb_conda_kernels. Sometimes this command will error out. If it does, try again.\n",
+    "conda install -c conda-forge nb_conda_kernels"
    ]
   },
   {
@@ -564,7 +576,7 @@
    "outputs": [],
    "source": [
     "from IPython.display import IFrame\n",
-    "IFrame(\"quiz_files/quiz5-1.html\", width=600, height=250)"
+    "IFrame(\"quiz_files/quiz5-1.html\", width=600, height=350)"
    ]
   },
   {

diff --git a/GoogleCloud/submodule06_putting_it_all_together.ipynb b/GoogleCloud/submodule06_putting_it_all_together.ipynb
@@ -43,6 +43,18 @@
     "</div>"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "46d5fd0a-ed71-4fbf-82fa-0d40cbb3533a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%bash\n",
+    "# If there is still a missing module error, install nb_conda_kernels. Sometimes this command will error out. If it does, try again.\n",
+    "conda install -c conda-forge nb_conda_kernels"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -175,7 +187,7 @@
    "source": [
     "# FLASHCARD\n",
     "from IPython.display import IFrame\n",
-    "IFrame(\"quiz_files/quiz6-1.html\", width=600, height=250)"
+    "IFrame(\"quiz_files/quiz6-1.html\", width=600, height=350)"
    ]
   },
   {
@@ -311,7 +323,7 @@
    "source": [
     "# FLASHCARD\n",
     "from IPython.display import IFrame\n",
-    "IFrame(\"quiz_files/quiz6-2.html\", width=600, height=250)"
+    "IFrame(\"quiz_files/quiz6-2.html\", width=600, height=350)"
    ]
   },
   {
@@ -410,7 +422,7 @@
    "source": [
     "# FLASHCARD\n",
     "from IPython.display import IFrame\n",
-    "IFrame(\"quiz_files/quiz6-3.html\", width=600, height=250)"
+    "IFrame(\"quiz_files/quiz6-3.html\", width=600, height=350)"
    ]
   },
   {
@@ -449,7 +461,7 @@
    "source": [
     "# FLASHCARD\n",
     "from IPython.display import IFrame\n",
-    "IFrame(\"quiz_files/quiz6-4.html\", width=600, height=250)"
+    "IFrame(\"quiz_files/quiz6-4.html\", width=600, height=350)"
    ]
   },
   {

diff --git a/GoogleCloud/submodule07_error_mitigation.ipynb b/GoogleCloud/submodule07_error_mitigation.ipynb
@@ -156,7 +156,7 @@
    "source": [
     "# FLASHCARD\n",
     "from IPython.display import IFrame\n",
-    "IFrame(\"quiz_files/quiz7-1.html\", width=600, height=250)"
+    "IFrame(\"quiz_files/quiz7-1.html\", width=600, height=350)"
    ]
   },
   {
@@ -203,7 +203,7 @@
    "source": [
     "# FLASHCARD\n",
     "from IPython.display import IFrame\n",
-    "IFrame(\"quiz_files/quiz7-2.html\", width=600, height=250)"
+    "IFrame(\"quiz_files/quiz7-2.html\", width=600, height=350)"
    ]
   },
   {