From 03176d595203f0c9b220f21ee6319285a47b371e Mon Sep 17 00:00:00 2001 From: montgomerymt-NIH Date: Wed, 20 Nov 2024 11:41:41 -0500 Subject: [PATCH 01/11] Update submodule01_Intro_to_terminal.ipynb increased flashcard display height to show "next" button. --- GoogleCloud/submodule01_Intro_to_terminal.ipynb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/GoogleCloud/submodule01_Intro_to_terminal.ipynb b/GoogleCloud/submodule01_Intro_to_terminal.ipynb index a0602cd..130e1cd 100644 --- 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)" ] }, { From b8b2b43873e3202c08dce14273dc1f348591ffb5 Mon Sep 17 00:00:00 2001 From: montgomerymt-NIH Date: Wed, 20 Nov 2024 11:43:04 -0500 Subject: [PATCH 02/11] Update submodule03_genomics_file_format.ipynb flashcard display height --- GoogleCloud/submodule03_genomics_file_format.ipynb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/GoogleCloud/submodule03_genomics_file_format.ipynb b/GoogleCloud/submodule03_genomics_file_format.ipynb index 21426f3..dd47092 100644 --- 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)" ] }, { @@ -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)" ] }, { From d94ae1d08c57350b4bca80b45b40383d0da4a63b Mon Sep 17 00:00:00 2001 From: montgomerymt-NIH Date: Wed, 20 Nov 2024 11:43:45 -0500 Subject: [PATCH 03/11] Update submodule04_beyond_basic_bash.ipynb flashcard height --- GoogleCloud/submodule04_beyond_basic_bash.ipynb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/GoogleCloud/submodule04_beyond_basic_bash.ipynb b/GoogleCloud/submodule04_beyond_basic_bash.ipynb index 5455952..5def4e7 100644 --- 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)" ] }, { From ded395b539f286ec2f597b11a2a336b12a6c3150 Mon Sep 17 00:00:00 2001 From: montgomerymt-NIH Date: Wed, 20 Nov 2024 11:54:42 -0500 Subject: [PATCH 04/11] Update submodule06_putting_it_all_together.ipynb added installation for nb_conda_kernels flashcard height adjustment --- .../submodule06_putting_it_all_together.ipynb | 20 +++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/GoogleCloud/submodule06_putting_it_all_together.ipynb b/GoogleCloud/submodule06_putting_it_all_together.ipynb index 4d21928..29c4e03 100644 --- a/GoogleCloud/submodule06_putting_it_all_together.ipynb +++ b/GoogleCloud/submodule06_putting_it_all_together.ipynb @@ -43,6 +43,18 @@ "" ] }, + { + "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" + ] + }, { "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)" ] }, { From 11019329d79684f183f9f5d20290c0b43dbafaa3 Mon Sep 17 00:00:00 2001 From: montgomerymt-NIH Date: Wed, 20 Nov 2024 11:55:37 -0500 Subject: [PATCH 05/11] Update submodule07_error_mitigation.ipynb flashcard height adjustment --- GoogleCloud/submodule07_error_mitigation.ipynb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/GoogleCloud/submodule07_error_mitigation.ipynb b/GoogleCloud/submodule07_error_mitigation.ipynb index 2fee556..3ca03f7 100644 --- 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)" ] }, { From 193429bc90cecf67928ea8cec0a3844b9eee0948 Mon Sep 17 00:00:00 2001 From: montgomerymt-NIH Date: Wed, 20 Nov 2024 12:00:42 -0500 Subject: [PATCH 06/11] Update submodule06_putting_it_all_together.ipynb wording change for nb_kernels install --- GoogleCloud/submodule06_putting_it_all_together.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/GoogleCloud/submodule06_putting_it_all_together.ipynb b/GoogleCloud/submodule06_putting_it_all_together.ipynb index 29c4e03..9e735f8 100644 --- a/GoogleCloud/submodule06_putting_it_all_together.ipynb +++ b/GoogleCloud/submodule06_putting_it_all_together.ipynb @@ -51,7 +51,7 @@ "outputs": [], "source": [ "%%bash\n", - "# Install nb_conda_kernels. Sometimes this command will error out. If it does, try again.\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" ] }, From b08c5355c89d9eadf08450a3f4f5168791f12145 Mon Sep 17 00:00:00 2001 From: montgomerymt-NIH Date: Wed, 20 Nov 2024 12:11:40 -0500 Subject: [PATCH 07/11] Update submodule05_software_management.ipynb added installation for nb_conda_kernels --- GoogleCloud/submodule05_software_management.ipynb | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/GoogleCloud/submodule05_software_management.ipynb b/GoogleCloud/submodule05_software_management.ipynb index 383217f..4d5e8be 100644 --- a/GoogleCloud/submodule05_software_management.ipynb +++ b/GoogleCloud/submodule05_software_management.ipynb @@ -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" ] }, { From 486cf96903ec8a474c329f01232a9bd8b001e4f9 Mon Sep 17 00:00:00 2001 From: montgomerymt-NIH Date: Wed, 20 Nov 2024 12:12:16 -0500 Subject: [PATCH 08/11] Update submodule05_software_management.ipynb flashcard height --- GoogleCloud/submodule05_software_management.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/GoogleCloud/submodule05_software_management.ipynb b/GoogleCloud/submodule05_software_management.ipynb index 4d5e8be..c709e00 100644 --- a/GoogleCloud/submodule05_software_management.ipynb +++ b/GoogleCloud/submodule05_software_management.ipynb @@ -576,7 +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)" ] }, { From 3f29cc84a3d747da3db349a1f796b625f5c5d963 Mon Sep 17 00:00:00 2001 From: montgomerymt-NIH Date: Wed, 20 Nov 2024 12:19:35 -0500 Subject: [PATCH 09/11] Update submodule05_software_management.ipynb updated description for how to "cd into a directory" --- GoogleCloud/submodule05_software_management.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/GoogleCloud/submodule05_software_management.ipynb b/GoogleCloud/submodule05_software_management.ipynb index c709e00..c6b5e8d 100644 --- 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]." ] }, { From 6f00bddc1268db9ca9b9c542ce18ed6357a26325 Mon Sep 17 00:00:00 2001 From: montgomerymt-NIH Date: Wed, 20 Nov 2024 12:20:58 -0500 Subject: [PATCH 10/11] Update submodule05_software_management.ipynb formatting --- GoogleCloud/submodule05_software_management.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/GoogleCloud/submodule05_software_management.ipynb b/GoogleCloud/submodule05_software_management.ipynb index c6b5e8d..6db4b61 100644 --- 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. Open the terminal, type cd, then press [Enter]." + "cd into the directory outputed from the command above. Open the terminal, type `cd`, then press [Enter]." ] }, { From 5ea50c165204129d5641405a81581640dea43533 Mon Sep 17 00:00:00 2001 From: montgomerymt-NIH Date: Wed, 20 Nov 2024 12:33:32 -0500 Subject: [PATCH 11/11] Update submodule03_genomics_file_format.ipynb printing out 10000 base pairs makes the notebook unworkable. reduced to 100 --- GoogleCloud/submodule03_genomics_file_format.ipynb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/GoogleCloud/submodule03_genomics_file_format.ipynb b/GoogleCloud/submodule03_genomics_file_format.ipynb index dd47092..8766507 100644 --- a/GoogleCloud/submodule03_genomics_file_format.ipynb +++ b/GoogleCloud/submodule03_genomics_file_format.ipynb @@ -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' " ] }, {