Merge pull request #13 from NIGMS/links-round2

Links round2

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**
 

AWS/submodule01_Intro_to_terminal.ipynb

@@ -517,7 +517,7 @@
     "---------\n",
     "<div class=\"alert alert-block alert-danger\">\n",
     "    <i class=\"fa fa-exclamation-circle\" aria-hidden=\"true\"></i>\n",
-    "    <b>Alert: </b>  The following steps require that you use the terminal. For instructions on opening a new terminal console within current layout click <a href=\"https://github.com/NIGMS/NIGMS-Sandbox/blob/new_console_doc/docs/HowToCreateNewTerminalConsoleJupyterLab.md\">here</a> \n",
+    "    <b>Alert: </b>  The following steps require that you use the terminal. For instructions on opening a new terminal console within current layout click <a href=\"https://github.com/NIGMS/NIGMS-Sandbox/blob/main/docs/HowToCreateNewTerminalConsoleJupyterLab.md\">here</a> \n",
     "</div>\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",

AWS/submodule04_beyond_basic_bash.ipynb

@@ -275,7 +275,7 @@
     "\n",
     "<div class=\"alert alert-block alert-danger\">\n",
     "    <i class=\"fa fa-exclamation-circle\" aria-hidden=\"true\"></i>\n",
-    "    <b>Alert: </b>  The following steps require that you use the terminal. For instructions on opening a new terminal console within current layout click <a href=\"https://github.com/NIGMS/NIGMS-Sandbox/blob/new_console_doc/docs/HowToCreateNewTerminalConsoleJupyterLab.md\">here</a> \n",
+    "    <b>Alert: </b>  The following steps require that you use the terminal. For instructions on opening a new terminal console within current layout click <a href=\"https://github.com/NIGMS/NIGMS-Sandbox/blob/main/docs/HowToCreateNewTerminalConsoleJupyterLab.md\">here</a> \n",
     "</div>\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",

AWS/submodule05_software_management.ipynb

@@ -90,7 +90,7 @@
    "source": [
     "<div class=\"alert alert-block alert-danger\">\n",
     "    <i class=\"fa fa-exclamation-circle\" aria-hidden=\"true\"></i>\n",
-    "    <b>Alert: </b>  The following steps require that you use the terminal. For instructions on opening a new terminal console within current layout click <a href=\"https://github.com/NIGMS/NIGMS-Sandbox/blob/new_console_doc/docs/HowToCreateNewTerminalConsoleJupyterLab.md\">here</a> \n",
+    "    <b>Alert: </b>  The following steps require that you use the terminal. For instructions on opening a new terminal console within current layout click <a href=\"https://github.com/NIGMS/NIGMS-Sandbox/blob/main/docs/HowToCreateNewTerminalConsoleJupyterLab.md\">here</a> \n",
     "</div>\n"
    ]
   },

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**.  
 

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.
 
@@ -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)