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Source  : 91116c2
Branch  : main
Author  : Alexis Lucattini <[email protected]>
Time    : 2024-05-08 22:35:30 +0000
Message : Merge pull request #26 from umccr/enhancement/add-github-section

Added setup section on using github

files/data_setup.Rmd

@@ -5,18 +5,34 @@ You will need to download some example files for this lesson. In this tutorial w
 ### Setting up a practice Git repository
 
 For this tutorial some existing tools are needed to build the workflow. These existing tools will be imported via GitHub.
-First we need to create an empty git repository for all our files. To do this, use this command:
+
+
+#### Make a repository on GitHub.com
+
+Head to [github.com/new][github_new_repo] and create a new repository.  
+
+Name it `novice-tutorial-exercises`.  
+
+Make sure the repository is `public`.  
+
+Check 'Add a README file', and choose `GNU General Public License v3.0` as your license.
+
+#### Clone the repository
 
 ```bash
-git init novice-tutorial-exercises
+git clone [email protected]/YOUR_GITHUB_USERNAME/novice-tutorial-exercises
 ```
 
-Next, we need to move into our empty git repo:
+Next, we need to move into our git repo:
 
 ```bash
 cd novice-tutorial-exercises
 ```
 
+<br>
+
+#### Add in bio-cwl-tools as a submodule
+
 Then import bio-cwl-tools with this command:
 
 ```bash
@@ -25,6 +41,7 @@ git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
 
 <br>
 
+
 ### Downloading sample and reference data
 
 Create a new directory inside the `novice-tutorial-exercises` directory and download the data:
@@ -61,6 +78,16 @@ We should exclude the rnaseq folder from being tracked in this repository.
 echo 'rnaseq/' >> .gitignore
 ```
 
+### Add .gitignore to git
+
+`.gitignore` is a file that is tracked like all other GitHub commands.  
+
+```
+git add .gitignore
+git commit -m "Don't track files in the rnaseq directory"
+git push
+```
+
 <br>
 
 ### STAR Genome index
@@ -303,4 +330,4 @@ Then retry the `md5sum` command
 
 [dos2unix]: https://phoenixnap.com/kb/convert-dos-to-unix
 [checksum_wiki]: https://en.wikipedia.org/wiki/Checksum
-
+[github_new_repo]: https://github.com/new

files/github.Rmd

@@ -0,0 +1,67 @@
+## GitHub Requirements
+
+This part assumes you have a GitHub.com account.  
+
+If you do not have a GitHub.com account you can create one [here][github_signup]
+
+The following steps will take you through the process of creating a SSH key pair to 
+connect your terminal to GitHub. If you already have this set up, you may skip this part.  
+
+
+:::::::::::::::::: callout
+
+
+### Opening files from the terminal
+
+Whenever you are required to open a file from the terminal, you may type `code /path/to/file`.
+
+This will also create the file if it does not yet exist.  
+
+::::::::::::::::::
+
+
+### SSH Key
+
+After generating an account you will need to generate an SSH Key so that you can pull and push code from your terminal to GitHub.  
+
+In your terminal run the following command
+
+```
+# Create the .ssh directory
+mkdir -p --mode 700 ~/.ssh
+
+ssh-keygen -f ~/.ssh/github -t ed25519 -q -N ""
+```
+
+### Add your public key to GitHub
+
+Head to [GitHub SSH and GPG keys][github_settings].  
+
+Click `New SSH key`.  
+set the title as the name of your computer (this can be anything), and under the 'Key', 
+copy the contents of `~/.ssh/github.pub` from your terminal.  
+
+### Setting your SSH Config
+
+Open up `~/.ssh/config` and add in the following code chunk:
+
+```
+Host github.com
+  IdentityFile /home/YOUR_USER_NAME/.ssh/github
+  User git
+```
+
+### Test your connection
+
+```
+ssh -T [email protected]
+```
+
+You should see a message like so
+
+```
+Hi alexiswl! You've successfully authenticated, but GitHub does not provide shell access.
+```
+
+[github_signup]: https://github.com/signup
+[github_settings]: https://github.com/settings/keys

md5sum.txt

@@ -11,7 +11,7 @@
 "episodes/addendum-01-debug.Rmd" "3ce548abd8cb1934aa12b16cd62104e3" "site/built/addendum-01-debug.md" "2024-05-08"
 "episodes/more_info.md" "b97f3b7186f568f33352041b7e2449ff" "site/built/more_info.md" "2024-05-08"
 "instructors/instructor-notes.md" "cae72b6712578d74a49fea7513099f8c" "site/built/instructor-notes.md" "2024-05-08"
-"learners/setup.Rmd" "cd2c452313fbbb2db56ed77768f8f2a8" "site/built/setup.md" "2024-05-08"
+"learners/setup.Rmd" "6020a6e393ac568a958d4a536d063984" "site/built/setup.md" "2024-05-08"
 "old_carpentries_incubator/404.md" "5e864846045fca3e8d82fa69eaefa5f0" "site/built/404.md" "2024-05-08"
 "old_carpentries_incubator/aio.md" "18553f83976668567aa30777afd7c719" "site/built/aio.md" "2024-05-08"
 "old_carpentries_incubator/reference.md" "0e582dab8c7f586fb96bb1dcf1ca6b4c" "site/built/reference.md" "2024-05-08"

setup.md

@@ -501,25 +501,111 @@ docker pull quay.io/biocontainers/subread:2.0.6--he4a0461_0
 ```
 
 
+
+## GitHub Requirements
+
+This part assumes you have a GitHub.com account.  
+
+If you do not have a GitHub.com account you can create one [here][github_signup]
+
+The following steps will take you through the process of creating a SSH key pair to 
+connect your terminal to GitHub. If you already have this set up, you may skip this part.  
+
+
+:::::::::::::::::: callout
+
+
+### Opening files from the terminal
+
+Whenever you are required to open a file from the terminal, you may type `code /path/to/file`.
+
+This will also create the file if it does not yet exist.  
+
+::::::::::::::::::
+
+
+### SSH Key
+
+After generating an account you will need to generate an SSH Key so that you can pull and push code from your terminal to GitHub.  
+
+In your terminal run the following command
+
+```
+# Create the .ssh directory
+mkdir -p --mode 700 ~/.ssh
+
+ssh-keygen -f ~/.ssh/github -t ed25519 -q -N ""
+```
+
+### Add your public key to GitHub
+
+Head to [GitHub SSH and GPG keys][github_settings].  
+
+Click `New SSH key`.  
+set the title as the name of your computer (this can be anything), and under the 'Key', 
+copy the contents of `~/.ssh/github.pub` from your terminal.  
+
+### Setting your SSH Config
+
+Open up `~/.ssh/config` and add in the following code chunk:
+
+```
+Host github.com
+  IdentityFile /home/YOUR_USER_NAME/.ssh/github
+  User git
+```
+
+### Test your connection
+
+```
+ssh -T [email protected]
+```
+
+You should see a message like so
+
+```
+Hi alexiswl! You've successfully authenticated, but GitHub does not provide shell access.
+```
+
+[github_signup]: https://github.com/signup
+[github_settings]: https://github.com/settings/keys
+
+
 ## Data Requirements
 
 You will need to download some example files for this lesson. In this tutorial we will use RNA sequencing data.
 
 ### Setting up a practice Git repository
 
 For this tutorial some existing tools are needed to build the workflow. These existing tools will be imported via GitHub.
-First we need to create an empty git repository for all our files. To do this, use this command:
+
+
+#### Make a repository on GitHub.com
+
+Head to [github.com/new][github_new_repo] and create a new repository.  
+
+Name it `novice-tutorial-exercises`.  
+
+Make sure the repository is `public`.  
+
+Check 'Add a README file', and choose `GNU General Public License v3.0` as your license.
+
+#### Clone the repository
 
 ```bash
-git init novice-tutorial-exercises
+git clone [email protected]/YOUR_GITHUB_USERNAME/novice-tutorial-exercises
 ```
 
-Next, we need to move into our empty git repo:
+Next, we need to move into our git repo:
 
 ```bash
 cd novice-tutorial-exercises
 ```
 
+<br>
+
+#### Add in bio-cwl-tools as a submodule
+
 Then import bio-cwl-tools with this command:
 
 ```bash
@@ -528,6 +614,7 @@ git submodule add https://github.com/common-workflow-library/bio-cwl-tools.git
 
 <br>
 
+
 ### Downloading sample and reference data
 
 Create a new directory inside the `novice-tutorial-exercises` directory and download the data:
@@ -564,6 +651,16 @@ We should exclude the rnaseq folder from being tracked in this repository.
 echo 'rnaseq/' >> .gitignore
 ```
 
+### Add .gitignore to git
+
+`.gitignore` is a file that is tracked like all other GitHub commands.  
+
+```
+git add .gitignore
+git commit -m "Don't track files in the rnaseq directory"
+git push
+```
+
 <br>
 
 ### STAR Genome index
@@ -806,4 +903,4 @@ Then retry the `md5sum` command
 
 [dos2unix]: https://phoenixnap.com/kb/convert-dos-to-unix
 [checksum_wiki]: https://en.wikipedia.org/wiki/Checksum
-
+[github_new_repo]: https://github.com/new