From eaaacea140fe3b10c2ed7cab56e975e516afd484 Mon Sep 17 00:00:00 2001 From: RossCampbellNIH2 Date: Wed, 13 Nov 2024 16:56:35 -0600 Subject: [PATCH 01/10] Update README.md fix links to GCP/AWS dirs --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 169687c..782846e 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ # Dartmouth College Bioinformatics for Beginners --------------------------------- -This module introduces you to the [Bash shell scripting language](https://en.wikipedia.org/wiki/Bash_(Unix_shell)), working with common genomics file formats, and working within the terminal environment. In addition to the overview given in this README you will find 6 submodules in the forms of Jupyter notebooks that teach you different components of working with genomics data in the cloud. This module can be run on either [Google Cloud Platform (GCP)](https://github.com/NIGMS/Fundamentals-of-Bioinformatics/blob/Ross_readmes/GoogleCloud/) or [Amazon Web Services (AWS)](https://github.com/NIGMS/Fundamentals-of-Bioinformatics/blob/Ross_readmes/AWS/) +This module introduces you to the [Bash shell scripting language](https://en.wikipedia.org/wiki/Bash_(Unix_shell)), working with common genomics file formats, and working within the terminal environment. In addition to the overview given in this README you will find 6 submodules in the forms of Jupyter notebooks that teach you different components of working with genomics data in the cloud. This module can be run on either [Google Cloud Platform (GCP)](https://github.com/NIGMS/Fundamentals-of-Bioinformatics/tree/main/GoogleCloud/) or [Amazon Web Services (AWS)](https://github.com/NIGMS/Fundamentals-of-Bioinformatics/tree/main/AWS/) Watch this [Introduction Video](https://www.youtube.com/watch?v=VaZedZhjXrU&list=PLXaEJPtnQ4w7Vu7vqWbttBjUGrPp4Qa7b&index=1) to learn more about the module. From 5be961fcff95c9a4c57c9d29a658f01c632b0377 Mon Sep 17 00:00:00 2001 From: RossCampbellNIH2 Date: Wed, 13 Nov 2024 17:09:27 -0600 Subject: [PATCH 02/10] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 782846e..0f20a79 100644 --- a/README.md +++ b/README.md @@ -62,7 +62,7 @@ This resource was supported with funds from NIH grant P20GM130454 and NIH grant ## **License for Data** -Text and materials are licensed under a Creative Commons CC-BY-NC-SA license. The license allows you to copy, remix and redistribute any of our publicly available materials, under the condition that you attribute the work (details in the license) and do not make profits from it. More information is available [here](https://tilburgsciencehub.com/about/#license). +Text and materials are licensed under a Creative Commons CC-BY-NC-SA license. The license allows you to copy, remix and redistribute any of our publicly available materials, under the condition that you attribute the work (details in the license) and do not make profits from it. More information is available [here](https://tilburgsciencehub.com/about/). ![Creative commons license](images/licensebuttons.png) From a92cfd9fb3e59616902f7cdd713d1176ca9cefe9 Mon Sep 17 00:00:00 2001 From: RossCampbellNIH2 Date: Wed, 13 Nov 2024 17:14:09 -0600 Subject: [PATCH 03/10] Update submodule05_software_management.ipynb Update link to HowToCreateNewTerminalConsoleJupyterLab.md --- AWS/submodule05_software_management.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/AWS/submodule05_software_management.ipynb b/AWS/submodule05_software_management.ipynb index c065a2a..a4f3a2d 100644 --- a/AWS/submodule05_software_management.ipynb +++ b/AWS/submodule05_software_management.ipynb @@ -90,7 +90,7 @@ "source": [ "
\n", " \n", - " Alert: The following steps require that you use the terminal. For instructions on opening a new terminal console within current layout click here \n", + " Alert: The following steps require that you use the terminal. For instructions on opening a new terminal console within current layout click here \n", "
\n" ] }, From d01e2060aae4ccb7924822bfe3d758c08060e123 Mon Sep 17 00:00:00 2001 From: RossCampbellNIH2 Date: Wed, 13 Nov 2024 17:22:37 -0600 Subject: [PATCH 04/10] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 0f20a79..2f6f20a 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ # Dartmouth College Bioinformatics for Beginners --------------------------------- -This module introduces you to the [Bash shell scripting language](https://en.wikipedia.org/wiki/Bash_(Unix_shell)), working with common genomics file formats, and working within the terminal environment. In addition to the overview given in this README you will find 6 submodules in the forms of Jupyter notebooks that teach you different components of working with genomics data in the cloud. This module can be run on either [Google Cloud Platform (GCP)](https://github.com/NIGMS/Fundamentals-of-Bioinformatics/tree/main/GoogleCloud/) or [Amazon Web Services (AWS)](https://github.com/NIGMS/Fundamentals-of-Bioinformatics/tree/main/AWS/) +This module introduces you to the [Bash shell scripting language](https://en.wikipedia.org/wiki/Bash_(Unix_shell))), working with common genomics file formats, and working within the terminal environment. In addition to the overview given in this README you will find 6 submodules in the forms of Jupyter notebooks that teach you different components of working with genomics data in the cloud. This module can be run on either [Google Cloud Platform (GCP)](https://github.com/NIGMS/Fundamentals-of-Bioinformatics/tree/main/GoogleCloud/) or [Amazon Web Services (AWS)](https://github.com/NIGMS/Fundamentals-of-Bioinformatics/tree/main/AWS/) Watch this [Introduction Video](https://www.youtube.com/watch?v=VaZedZhjXrU&list=PLXaEJPtnQ4w7Vu7vqWbttBjUGrPp4Qa7b&index=1) to learn more about the module. From 92c680823a97e34228adfd23b32fa8b165ed7409 Mon Sep 17 00:00:00 2001 From: RossCampbellNIH2 Date: Thu, 14 Nov 2024 20:08:36 -0600 Subject: [PATCH 05/10] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 2f6f20a..0f20a79 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ # Dartmouth College Bioinformatics for Beginners --------------------------------- -This module introduces you to the [Bash shell scripting language](https://en.wikipedia.org/wiki/Bash_(Unix_shell))), working with common genomics file formats, and working within the terminal environment. In addition to the overview given in this README you will find 6 submodules in the forms of Jupyter notebooks that teach you different components of working with genomics data in the cloud. This module can be run on either [Google Cloud Platform (GCP)](https://github.com/NIGMS/Fundamentals-of-Bioinformatics/tree/main/GoogleCloud/) or [Amazon Web Services (AWS)](https://github.com/NIGMS/Fundamentals-of-Bioinformatics/tree/main/AWS/) +This module introduces you to the [Bash shell scripting language](https://en.wikipedia.org/wiki/Bash_(Unix_shell)), working with common genomics file formats, and working within the terminal environment. In addition to the overview given in this README you will find 6 submodules in the forms of Jupyter notebooks that teach you different components of working with genomics data in the cloud. This module can be run on either [Google Cloud Platform (GCP)](https://github.com/NIGMS/Fundamentals-of-Bioinformatics/tree/main/GoogleCloud/) or [Amazon Web Services (AWS)](https://github.com/NIGMS/Fundamentals-of-Bioinformatics/tree/main/AWS/) Watch this [Introduction Video](https://www.youtube.com/watch?v=VaZedZhjXrU&list=PLXaEJPtnQ4w7Vu7vqWbttBjUGrPp4Qa7b&index=1) to learn more about the module. From 7dda6d4f94142e6e490361489f73a46da518c43f Mon Sep 17 00:00:00 2001 From: RossCampbellNIH2 Date: Thu, 14 Nov 2024 20:42:05 -0600 Subject: [PATCH 06/10] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 0f20a79..bb3118e 100644 --- a/README.md +++ b/README.md @@ -62,7 +62,7 @@ This resource was supported with funds from NIH grant P20GM130454 and NIH grant ## **License for Data** -Text and materials are licensed under a Creative Commons CC-BY-NC-SA license. The license allows you to copy, remix and redistribute any of our publicly available materials, under the condition that you attribute the work (details in the license) and do not make profits from it. More information is available [here](https://tilburgsciencehub.com/about/). +Text and materials are licensed under a Creative Commons CC-BY-NC-SA license. The license allows you to copy, remix and redistribute any of our publicly available materials, under the condition that you attribute the work (details in the license) and do not make profits from it. More information is available [here](https://tilburgsciencehub.com/about). ![Creative commons license](images/licensebuttons.png) From 70db45db7eecf7c478a2f36e9caee294c58caa08 Mon Sep 17 00:00:00 2001 From: RossCampbellNIH2 Date: Thu, 14 Nov 2024 20:44:30 -0600 Subject: [PATCH 07/10] Update submodule04_beyond_basic_bash.ipynb fixing branch in https://github.com/NIGMS/NIGMS-Sandbox/blob/main/docs/HowToCreateNewTerminalConsoleJupyterLab.md --- AWS/submodule04_beyond_basic_bash.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/AWS/submodule04_beyond_basic_bash.ipynb b/AWS/submodule04_beyond_basic_bash.ipynb index a169bdc..76ab966 100644 --- a/AWS/submodule04_beyond_basic_bash.ipynb +++ b/AWS/submodule04_beyond_basic_bash.ipynb @@ -275,7 +275,7 @@ "\n", "
\n", " \n", - " Alert: The following steps require that you use the terminal. For instructions on opening a new terminal console within current layout click here \n", + " Alert: The following steps require that you use the terminal. For instructions on opening a new terminal console within current layout click here \n", "
\n", "\n", "Loops are pretty useful, but what if we wanted to make it even simpler to run this code. Maybe we even want to share the program we just wrote with other lab members so that they can execute it on their own FASTQ files. One way to do this would be to write this series of commands into a `Bash script`, that can be executed at the command line, passing the files you would like to be operated on to the script.\n", From 8167ef89c95d0c1ef6433907a86bdedd57e85a86 Mon Sep 17 00:00:00 2001 From: RossCampbellNIH2 Date: Thu, 14 Nov 2024 21:15:31 -0600 Subject: [PATCH 08/10] Update README.md removing AWS-specific git clone command --- AWS/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/AWS/README.md b/AWS/README.md index c689587..e13bf48 100644 --- a/AWS/README.md +++ b/AWS/README.md @@ -19,7 +19,7 @@ Included here are several submodules or tutorials in the form of Jupyter noteboo Follow the steps highlighted [here](https://github.com/NIGMS/NIGMS-Sandbox/blob/main/docs/HowToCreateAWSSagemakerNotebooks.md) to create a new notebook instance in AWS SageMaker. For this module you should select Linux 2 and Python 3 in the Environment. In the Notebook instance type tab, select ml.t3.2xlarge from the dropdown box and set volume size to 20 GB. It is **important to shut down** the kernel at the end of your work to avoid getting charged. -To use our module, open a new Terminal window from your new notebook instance and clone this repo using `git clone https://github.com/NIGMS/Fundamentals-of-Bioinformatics/AWS.git`. Navigate to the directory for this project. You will then see the notebooks in your environment. +To use our module, open a new Terminal window from your new notebook instance and clone this repo using `git clone https://github.com/NIGMS/Fundamentals-of-Bioinformatics.git`. Navigate to the directory for this project. You will then see the notebooks in your environment. ## **Software Requirements** From b265ff7d2e4d66dd978706f1ae818723abc10f95 Mon Sep 17 00:00:00 2001 From: RossCampbellNIH2 Date: Thu, 14 Nov 2024 21:16:26 -0600 Subject: [PATCH 09/10] Update README.md --- GoogleCloud/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/GoogleCloud/README.md b/GoogleCloud/README.md index 759f957..c385407 100644 --- a/GoogleCloud/README.md +++ b/GoogleCloud/README.md @@ -19,7 +19,7 @@ Included here are several submodules or tutorials in the form of Jupyter noteboo Follow the steps highlighted [here](https://github.com/NIGMS/NIGMS-Sandbox/blob/main/docs/HowToCreateVertexAINotebooks.md) to create a new notebook instance in Vertex AI. Follow steps 1-8 and be especially careful to enable idle shutdown as highlighted in step 8. In step 7 in the Machine type tab, select n1-standard-4 from the dropdown box. -To use our module, open a new Terminal window from your new notebook instance and clone this repo using `git clone https://github.com/NIGMS/Fundamentals-of-Bioinformatics/GoogleCloud.git`. Navigate to the directory for this project. You will then see the notebooks in your environment. +To use our module, open a new Terminal window from your new notebook instance and clone this repo using `git clone https://github.com/NIGMS/Fundamentals-of-Bioinformatics.git`. Navigate to the directory for this project. You will then see the notebooks in your environment. Before you begin navigating the submodules you will need to enable extensions in the Jupyter notebook. To do this you can click on the puzzle piece icon ![enable extensions](images/extension.png) on the left most menu (down the side of the Jupyter notebook) and click on the red button that says **Enable**. From 465568f998847efcf94986c38c58a00cced47b61 Mon Sep 17 00:00:00 2001 From: RossCampbellNIH2 Date: Thu, 14 Nov 2024 21:20:43 -0600 Subject: [PATCH 10/10] Update submodule01_Intro_to_terminal.ipynb --- AWS/submodule01_Intro_to_terminal.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/AWS/submodule01_Intro_to_terminal.ipynb b/AWS/submodule01_Intro_to_terminal.ipynb index 2561d2f..06da15e 100644 --- a/AWS/submodule01_Intro_to_terminal.ipynb +++ b/AWS/submodule01_Intro_to_terminal.ipynb @@ -517,7 +517,7 @@ "---------\n", "
\n", " \n", - " Alert: The following steps require that you use the terminal. For instructions on opening a new terminal console within current layout click here \n", + " Alert: The following steps require that you use the terminal. For instructions on opening a new terminal console within current layout click here \n", "
\n", "\n", "You might have noticed that all of my filenames use `_` or `-` to separate words rather than spaces. Within commands spaces are generally used to separate arguments. Spaces within filenames will need to be *escaped* with the back slash symbol `\\`in the terminal environment. That is we will need to explicitly indicate that the space is part of the filename and NOT an indication that a second argument is being provided to the command.\n",