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Updating the chipster-microbial repo (CSC internal instructions): | ||
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This repository contains the exercises of the microbial community analysis courses with Chipster | ||
(+ some related materials). | ||
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1. Access: | ||
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Ask an owner for access to the csc-training repo if you are not already a member. | ||
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2. Structure of the repo: | ||
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markdown: R markdown files for the exercises | ||
MiSeq: MiSeq 16S exercises | ||
IonTorrent: Ion Torrent 16S exercises | ||
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docs: html versions of the same markdown files (can be linked to course participants) | ||
note: the repo is configured with Github Pages to look for the displayed files in | ||
the docs folder in root (this can be changed in Settings) | ||
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README.md: determines what is shown on the front page | ||
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Getting started with Github Pages that the site is based on: | ||
https://docs.github.com/en/pages/getting-started-with-github-pages/creating-a-github-pages-site | ||
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3. Editing the materials: | ||
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Because the markdown files need to be converted to html, the easiest way is to edit the markdown | ||
files on your own computer, convert into html and then upload both files to Github (markdown in | ||
the folder markdown, html in the folder docs). | ||
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3.1 Start with 'git clone [path of the repo]' on your own terminal. Find the path of the repo on | ||
the front page under Code -> ssh. For this you should have ssh keys set up for git/Github. | ||
To update an existing repo on your computer, use 'git pull' in the repo directory. | ||
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3.2 After cloning, navigate to the repo folder and make a new branch: | ||
cd newrepo | ||
git checkout -b yourbranch | ||
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3.3 Make the changes in the R Markdown file on your own computer. Convert the markdown file into html. For example in RStudio, use 'Knit' to create the html. Move the html file to the 'docs' folder. | ||
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3.4 Submit the changes to Github: | ||
git add -A | ||
git commit -m "message about what has been changed" | ||
git branch [to double check the branch name for the next command] | ||
git push origin -u yourbranch | ||
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-> copy and open the web address from the output, create a pull request in Github, merge. Done! | ||
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