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hadiparsianNIHhadiparsianNIH
authored
moved quiz to the main folder
1 parent f423386 commit 1deb650

34 files changed

Lines changed: 81 additions & 474 deletions

‎AWS/Submodule_00_background.ipynb‎

Lines changed: 8 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -109,7 +109,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"display_quiz(\"quiz-material/00-pc1.json\")"
112+
"display_quiz(\"../quiz-material/00-pc1.json\")"
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]
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},
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{
@@ -281,7 +281,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"display_quiz(\"quiz-material/00-cp1.json\", shuffle_questions = True)"
284+
"display_quiz(\"../quiz-material/00-cp1.json\", shuffle_questions = True)"
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]
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},
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{
@@ -407,7 +407,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"display_quiz(\"quiz-material/00-cp2.json\", shuffle_questions = True)"
410+
"display_quiz(\"../quiz-material/00-cp2.json\", shuffle_questions = True)"
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]
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},
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{
@@ -444,7 +444,11 @@
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]
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}
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],
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"metadata": {},
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"metadata": {
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"language_info": {
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"name": "python"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎AWS/Submodule_01_prog_setup.ipynb‎

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -377,7 +377,7 @@
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"outputs": [],
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"source": [
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"from jupyterquiz import display_quiz\n",
380-
"display_quiz(\"Transcriptome-Assembly-Refinement-and-Applications/quiz-material/01-cp1.json\", shuffle_questions = True)"
380+
"display_quiz(\"../quiz-material/01-cp1.json\", shuffle_questions = True)"
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]
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},
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{
@@ -401,7 +401,11 @@
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]
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}
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],
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"metadata": {},
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"metadata": {
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"language_info": {
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"name": "python"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎AWS/Submodule_02_basic_assembly.ipynb‎

Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -320,8 +320,8 @@
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"outputs": [],
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"source": [
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"from jupytercards import display_flashcards\n",
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"display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/02-cp1-1.json')\n",
324-
"display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/02-cp1-2.json')"
323+
"display_flashcards('../quiz-material/02-cp1-1.json')\n",
324+
"display_flashcards('../quiz-material/02-cp1-2.json')"
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]
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},
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{
@@ -345,7 +345,11 @@
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]
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}
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],
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"metadata": {},
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"metadata": {
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"language_info": {
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"name": "python"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎AWS/Submodule_03_annotation_only.ipynb‎

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -445,7 +445,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/03-cp1-2.json')"
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"display_flashcards('../quiz-material/03-cp1-2.json')"
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]
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},
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{
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]
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}
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],
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"metadata": {},
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"metadata": {
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"language_info": {
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"name": "python"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎AWS/Submodule_04_google_batch_assembly.ipynb‎

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Original file line numberDiff line numberDiff line change
@@ -506,9 +506,9 @@
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"outputs": [],
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"source": [
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"from jupytercards import display_flashcards\n",
509-
"display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/04-cp1-2.json')\n",
510-
"display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/04-cp1-3.json')\n",
511-
"display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/04-cp1-4.json')"
509+
"display_flashcards('../quiz-material/04-cp1-2.json')\n",
510+
"display_flashcards('../quiz-material/04-cp1-3.json')\n",
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"display_flashcards('../quiz-material/04-cp1-4.json')"
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]
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},
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{
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]
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}
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],
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"metadata": {},
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"metadata": {
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"language_info": {
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"name": "python"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎GoogleCloud/Submodule_00_background.ipynb‎

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Original file line numberDiff line numberDiff line change
@@ -109,7 +109,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"display_quiz(\"quiz-material/00-pc1.json\")"
112+
"display_quiz(\"../quiz-material/00-pc1.json\")"
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"display_quiz(\"quiz-material/00-cp1.json\", shuffle_questions = True)"
284+
"display_quiz(\"../quiz-material/00-cp1.json\", shuffle_questions = True)"
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
410-
"display_quiz(\"quiz-material/00-cp2.json\", shuffle_questions = True)"
410+
"display_quiz(\"../quiz-material/00-cp2.json\", shuffle_questions = True)"
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]
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},
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{
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]
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}
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],
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"metadata": {},
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"metadata": {
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"language_info": {
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"name": "python"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎GoogleCloud/Submodule_01_prog_setup.ipynb‎

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -377,7 +377,7 @@
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"outputs": [],
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"source": [
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"from jupyterquiz import display_quiz\n",
380-
"display_quiz(\"Transcriptome-Assembly-Refinement-and-Applications/quiz-material/01-cp1.json\", shuffle_questions = True)"
380+
"display_quiz(\"../quiz-material/01-cp1.json\", shuffle_questions = True)"
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]
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},
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{
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]
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}
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],
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"metadata": {},
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"metadata": {
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"language_info": {
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"name": "python"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎GoogleCloud/Submodule_02_basic_assembly.ipynb‎

Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -320,8 +320,8 @@
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"outputs": [],
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"source": [
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"from jupytercards import display_flashcards\n",
323-
"display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/02-cp1-1.json')\n",
324-
"display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/02-cp1-2.json')"
323+
"display_flashcards('../quiz-material/02-cp1-1.json')\n",
324+
"display_flashcards('../quiz-material/02-cp1-2.json')"
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]
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},
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{
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]
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}
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],
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"metadata": {},
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"metadata": {
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"language_info": {
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"name": "python"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎GoogleCloud/Submodule_03_annotation_only.ipynb‎

Lines changed: 17 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -108,7 +108,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"!pwd"
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"! pwd"
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"!grep -c \">\" ./resources/trans/Oncorhynchus_mykiss_GGBN01.1.fa"
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"! grep -c \">\" ./resources/trans/Oncorhynchus_mykiss_GGBN01.1.fa"
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"!perl -i.allloc -pe 's/basicRun/onlyAnnRun/g' ./TransPi/nextflow.config"
179+
"! perl -i.allloc -pe 's/basicRun/onlyAnnRun/g' ./TransPi/nextflow.config"
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"!NXF_VER=22.10.1 ./nextflow run ./TransPi/TransPi.nf \\\n",
232+
"! NXF_VER=22.10.1 ./nextflow run ./TransPi/TransPi.nf \\\n",
233233
"-profile docker --onlyAnn "
234234
]
235235
},
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"metadata": {},
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"outputs": [],
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"source": [
251-
"!ls -l ./onlyAnnRun/output"
251+
"! ls -l ./onlyAnnRun/output"
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"!cat ./onlyAnnRun/output/RUN_INFO.txt"
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"! cat ./onlyAnnRun/output/RUN_INFO.txt"
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"!docker images"
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"! docker images"
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"!docker run -it --rm --volume /home:/home quay.io/biocontainers/busco:5.4.3--pyhdfd78af_0 busco --help"
324+
"! docker run -it --rm --volume /home:/home quay.io/biocontainers/busco:5.4.3--pyhdfd78af_0 busco --help"
325325
]
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},
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{
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"source": [
366366
"numthreads=!lscpu | grep '^CPU(s)'| awk '{print $2-1}'\n",
367367
"THREADS = int(numthreads[0])\n",
368-
"!echo $THREADS"
368+
"! echo $THREADS"
369369
]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"!docker run -it --rm --volume /home:/home quay.io/biocontainers/busco:5.4.3--pyhdfd78af_0 busco \\\n",
378+
"! docker run -it --rm --volume /home:/home quay.io/biocontainers/busco:5.4.3--pyhdfd78af_0 busco \\\n",
379379
"-i /home/jupyter/resources/trans/Oncorhynchus_mykiss_GGBN01.1.fa \\\n",
380380
"-l vertebrata_odb10 -o GGBN01_busco_vertebrata \\\n",
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"--out_path /home/jupyter/buscoOutput -m tran -c $THREADS"
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"outputs": [],
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"source": [
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"from jupytercards import display_flashcards\n",
428-
"display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/03-cp1-1.json')"
428+
"display_flashcards('../quiz-material/03-cp1-1.json')"
429429
]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/03-cp1-2.json')"
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"display_flashcards('../quiz-material/03-cp1-2.json')"
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]
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},
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{
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]
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}
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],
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"metadata": {},
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"metadata": {
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"language_info": {
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"name": "python"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎GoogleCloud/Submodule_04_google_batch_assembly.ipynb‎

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Original file line numberDiff line numberDiff line change
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"outputs": [],
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"source": [
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"from jupytercards import display_flashcards\n",
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"display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/04-cp1-2.json')\n",
510-
"display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/04-cp1-3.json')\n",
511-
"display_flashcards('Transcriptome-Assembly-Refinement-and-Applications/quiz-material/04-cp1-4.json')"
509+
"display_flashcards('../quiz-material/04-cp1-2.json')\n",
510+
"display_flashcards('../quiz-material/04-cp1-3.json')\n",
511+
"display_flashcards('../quiz-material/04-cp1-4.json')"
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]
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},
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{
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]
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}
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],
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"metadata": {},
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"metadata": {
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"language_info": {
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"name": "python"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

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