Merge pull request #8 from csc-training/IonTorrentJYU23

Update repo structure
csc-training · Sep 13, 2023 · 69a941f · 69a941f
2 parents 086f7cc + 8623cb5
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diff --git a/README.md b/README.md
@@ -8,9 +8,9 @@
 
 [Lecture videos (May 2021)](https://www.youtube.com/playlist?list=PLjiXAZO27elBjPaknlze6BkxebpEuj9KL)
 
-[Day 1 exercise sheet](https://csc-training.github.io/chipster-microbial/exercises/d1.html)
+[Day 1 exercise sheet](https://csc-training.github.io/chipster-microbial/MiSeq/Exercises_MiSeq_day1.html)
 
-[Day 2 exercise sheet](https://csc-training.github.io/chipster-microbial/exercises/d2.html)
+[Day 2 exercise sheet](https://csc-training.github.io/chipster-microbial/MiSeq/Exercises_MiSeq_day2.html)
 
 ---
 

diff --git a/docs/exercises/d1.html → docs/MiSeq/Exercises_day1.html b/docs/exercises/d1.html → docs/MiSeq/Exercises_day1.html
diff --git a/docs/exercises/d2.html → docs/MiSeq/Exercises_day2.html b/docs/exercises/d2.html → docs/MiSeq/Exercises_day2.html
diff --git a/docs/slides/d2.pdf → docs/MiSeq/slides/d2.pdf b/docs/slides/d2.pdf → docs/MiSeq/slides/d2.pdf
diff --git a/docs/video-transcripts/videos-d2.html → docs/MiSeq/video-transcripts/videos-d2.html b/docs/video-transcripts/videos-d2.html → docs/MiSeq/video-transcripts/videos-d2.html
diff --git a/eLena_md/updating_instructions.txt b/eLena_md/updating_instructions.txt
diff --git a/.../IonTorrent/Exercises_IonTorrent_day1.Rmd → .../IonTorrent/Exercises_IonTorrent_day1.Rmd b/.../IonTorrent/Exercises_IonTorrent_day1.Rmd → .../IonTorrent/Exercises_IonTorrent_day1.Rmd
diff --git a/.../IonTorrent/Exercises_IonTorrent_day2.Rmd → .../IonTorrent/Exercises_IonTorrent_day2.Rmd b/.../IonTorrent/Exercises_IonTorrent_day2.Rmd → .../IonTorrent/Exercises_IonTorrent_day2.Rmd
diff --git a/...onTorrent/Images/phenodata_IonTorrent.png → ...onTorrent/Images/phenodata_IonTorrent.png b/...onTorrent/Images/phenodata_IonTorrent.png → ...onTorrent/Images/phenodata_IonTorrent.png
diff --git a/...d/IonTorrent/Images/taxbar_IonTorrent.png → ...n/IonTorrent/Images/taxbar_IonTorrent.png b/...d/IonTorrent/Images/taxbar_IonTorrent.png → ...n/IonTorrent/Images/taxbar_IonTorrent.png
diff --git a/eLena_md/exercises-d1/d1.Rmd → markdown/MiSeq/Exercises_MiSeq_day1.Rmd b/eLena_md/exercises-d1/d1.Rmd → markdown/MiSeq/Exercises_MiSeq_day1.Rmd
diff --git a/eLena_md/exercises-d2/d2.Rmd → markdown/MiSeq/Exercises_MiSeq_day2.Rmd b/eLena_md/exercises-d2/d2.Rmd → markdown/MiSeq/Exercises_MiSeq_day2.Rmd
diff --git a/...a_md/exercises-d2/Images/pheno_layout.png → markdown/MiSeq/Images/pheno_layout.png b/...a_md/exercises-d2/Images/pheno_layout.png → markdown/MiSeq/Images/pheno_layout.png
diff --git a/eLena_md/exercises-d2/Images/taxbar.png → markdown/MiSeq/Images/taxbar.png b/eLena_md/exercises-d2/Images/taxbar.png → markdown/MiSeq/Images/taxbar.png
diff --git a/eLena_md/video-transcripts-d2/.Rhistory → ...down/MiSeq/video-transcripts-d2/.Rhistory b/eLena_md/video-transcripts-d2/.Rhistory → ...down/MiSeq/video-transcripts-d2/.Rhistory
diff --git a/eLena_md/video-transcripts-d2/videos-d2.Rmd → .../MiSeq/video-transcripts-d2/videos-d2.Rmd b/eLena_md/video-transcripts-d2/videos-d2.Rmd → .../MiSeq/video-transcripts-d2/videos-d2.Rmd
diff --git a/markdown/updating_instructions.txt b/markdown/updating_instructions.txt
@@ -0,0 +1,51 @@
+Updating the chipster-microbial repo (CSC internal instructions):
+
+This repository contains the exercises of the microbial community analysis courses with Chipster
+(+ some related materials).
+
+
+1. Access:
+
+Ask an owner for access to the csc-training repo if you are not already a member.
+
+
+2. Structure of the repo: 
+
+markdown: R markdown files for the exercises 
+	MiSeq: MiSeq 16S exercises
+	IonTorrent: Ion Torrent 16S exercises
+
+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)
+
+README.md: determines what is shown on the front page
+
+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
+
+
+3. Editing the materials: 
+
+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). 
+
+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.
+
+3.2 After cloning, navigate to the repo folder and make a new branch:
+cd newrepo
+git checkout -b yourbranch
+
+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.
+
+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
+
+-> copy and open the web address from the output, create a pull request in Github, merge. Done!
+