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A little meaty, but github doesn't support passwords on git pushes now so need to go the key route
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@@ -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 | ||
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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: | ||
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#### Make a repository on GitHub.com | ||
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Head to [github.com/new][github_new_repo] and create a new repository. | ||
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Name it `novice-tutorial-exercises`. | ||
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Make sure the repository is `public`. | ||
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Check 'Add a README file', and choose `GNU General Public License v3.0` as your license. | ||
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#### Clone the repository | ||
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```bash | ||
git init novice-tutorial-exercises | ||
git clone [email protected]/YOUR_GITHUB_USERNAME/novice-tutorial-exercises | ||
``` | ||
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Next, we need to move into our empty git repo: | ||
Next, we need to move into our git repo: | ||
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```bash | ||
cd novice-tutorial-exercises | ||
``` | ||
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<br> | ||
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#### Add in bio-cwl-tools as a submodule | ||
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Then import bio-cwl-tools with this command: | ||
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```bash | ||
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<br> | ||
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### Downloading sample and reference data | ||
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Create a new directory inside the `novice-tutorial-exercises` directory and download the data: | ||
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echo 'rnaseq/' >> .gitignore | ||
``` | ||
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### Add .gitignore to git | ||
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`.gitignore` is a file that is tracked like all other GitHub commands. | ||
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``` | ||
git add .gitignore | ||
git commit -m "Don't track files in the rnaseq directory" | ||
git push | ||
``` | ||
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<br> | ||
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### STAR Genome index | ||
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[dos2unix]: https://phoenixnap.com/kb/convert-dos-to-unix | ||
[checksum_wiki]: https://en.wikipedia.org/wiki/Checksum | ||
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[github_new_repo]: https://github.com/new |
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## GitHub Requirements | ||
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This part assumes you have a GitHub.com account. | ||
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If you do not have a GitHub.com account you can create one [here][github_signup] | ||
Check warning on line 5 in learners/files/github.Rmd GitHub Actions / Build markdown source files if valid
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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. | ||
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:::::::::::::::::: callout | ||
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### Opening files from the terminal | ||
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Whenever you are required to open a file from the terminal, you may type `code /path/to/file`. | ||
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This will also create the file if it does not yet exist. | ||
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:::::::::::::::::: | ||
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### SSH Key | ||
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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. | ||
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In your terminal run the following command | ||
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``` | ||
# Create the .ssh directory | ||
mkdir -p --mode 700 ~/.ssh | ||
ssh-keygen -f ~/.ssh/github -t ed25519 -q -N "" | ||
``` | ||
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### Add your public key to GitHub | ||
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Head to [GitHub SSH and GPG keys][github_settings]. | ||
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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. | ||
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### Setting your SSH Config | ||
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Open up `~/.ssh/config` and add in the following code chunk: | ||
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``` | ||
Host github.com | ||
IdentityFile /home/YOUR_USER_NAME/.ssh/github | ||
User git | ||
``` | ||
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### Test your connection | ||
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``` | ||
ssh -T [email protected] | ||
``` | ||
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You should see a message like so | ||
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``` | ||
Hi alexiswl! You've successfully authenticated, but GitHub does not provide shell access. | ||
``` | ||
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[github_signup]: https://github.com/signup | ||
[github_settings]: https://github.com/settings/keys |
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