From 8623cb509dd0fbe49a123ade486e63d622c69554 Mon Sep 17 00:00:00 2001 From: Heli Juottonen Date: Wed, 13 Sep 2023 14:46:10 +0300 Subject: [PATCH] Update repo structure --- README.md | 4 +- .../d1.html => MiSeq/Exercises_day1.html} | 0 .../d2.html => MiSeq/Exercises_day2.html} | 0 docs/{ => MiSeq}/slides/d2.pdf | Bin .../video-transcripts/videos-d2.html | 0 eLena_md/updating_instructions.txt | 18 ------- .../IonTorrent/Exercises_IonTorrent_day1.Rmd | 0 .../IonTorrent/Exercises_IonTorrent_day2.Rmd | 0 .../Images/phenodata_IonTorrent.png | Bin .../IonTorrent/Images/taxbar_IonTorrent.png | Bin .../MiSeq/Exercises_MiSeq_day1.Rmd | 0 .../MiSeq/Exercises_MiSeq_day2.Rmd | 0 .../MiSeq}/Images/pheno_layout.png | Bin .../MiSeq}/Images/taxbar.png | Bin .../MiSeq}/video-transcripts-d2/.Rhistory | 0 .../MiSeq}/video-transcripts-d2/videos-d2.Rmd | 0 markdown/updating_instructions.txt | 51 ++++++++++++++++++ 17 files changed, 53 insertions(+), 20 deletions(-) rename docs/{exercises/d1.html => MiSeq/Exercises_day1.html} (100%) rename docs/{exercises/d2.html => MiSeq/Exercises_day2.html} (100%) rename docs/{ => MiSeq}/slides/d2.pdf (100%) rename docs/{ => MiSeq}/video-transcripts/videos-d2.html (100%) delete mode 100644 eLena_md/updating_instructions.txt rename {eLena_md => markdown}/IonTorrent/Exercises_IonTorrent_day1.Rmd (100%) rename {eLena_md => markdown}/IonTorrent/Exercises_IonTorrent_day2.Rmd (100%) rename {eLena_md => markdown}/IonTorrent/Images/phenodata_IonTorrent.png (100%) rename {eLena_md => markdown}/IonTorrent/Images/taxbar_IonTorrent.png (100%) rename eLena_md/exercises-d1/d1.Rmd => markdown/MiSeq/Exercises_MiSeq_day1.Rmd (100%) rename eLena_md/exercises-d2/d2.Rmd => markdown/MiSeq/Exercises_MiSeq_day2.Rmd (100%) rename {eLena_md/exercises-d2 => markdown/MiSeq}/Images/pheno_layout.png (100%) rename {eLena_md/exercises-d2 => markdown/MiSeq}/Images/taxbar.png (100%) rename {eLena_md => markdown/MiSeq}/video-transcripts-d2/.Rhistory (100%) rename {eLena_md => markdown/MiSeq}/video-transcripts-d2/videos-d2.Rmd (100%) create mode 100644 markdown/updating_instructions.txt diff --git a/README.md b/README.md index 6ba453d..c42b458 100644 --- 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 b/docs/MiSeq/Exercises_day1.html similarity index 100% rename from docs/exercises/d1.html rename to docs/MiSeq/Exercises_day1.html diff --git a/docs/exercises/d2.html b/docs/MiSeq/Exercises_day2.html similarity index 100% rename from docs/exercises/d2.html rename to docs/MiSeq/Exercises_day2.html diff --git a/docs/slides/d2.pdf b/docs/MiSeq/slides/d2.pdf similarity index 100% rename from docs/slides/d2.pdf rename to docs/MiSeq/slides/d2.pdf diff --git a/docs/video-transcripts/videos-d2.html b/docs/MiSeq/video-transcripts/videos-d2.html similarity index 100% rename from docs/video-transcripts/videos-d2.html rename to docs/MiSeq/video-transcripts/videos-d2.html diff --git a/eLena_md/updating_instructions.txt b/eLena_md/updating_instructions.txt deleted file mode 100644 index ae634ab..0000000 --- a/eLena_md/updating_instructions.txt +++ /dev/null @@ -1,18 +0,0 @@ -Updating the chipster-microbial repo (CSC internal instructions): - -1. Access: - -Ask an owner for access to the csc-training repo if you are not already a member. - -2. Structure of the repo: - -eLena_md: R markdown files for the exercises etc. - exercises-d1, exercises-d2: MiSeq 16S materials - IonTorrent: Ion Torrent materials -docs: html versions of the same markdown files (can be linked to course participants) -README.md: determined what is shown on the front page - -3. Editing: - -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 eLena_md, html in the folder docs). So start with git clone on your own terminal. Create a new branch, make the changes in the markdown file (for example in RStudio), use 'knit' to convert into html, move the html file to the docs folder. Add, commit, push, create a pull request, merge. - diff --git a/eLena_md/IonTorrent/Exercises_IonTorrent_day1.Rmd b/markdown/IonTorrent/Exercises_IonTorrent_day1.Rmd similarity index 100% rename from eLena_md/IonTorrent/Exercises_IonTorrent_day1.Rmd rename to markdown/IonTorrent/Exercises_IonTorrent_day1.Rmd diff --git a/eLena_md/IonTorrent/Exercises_IonTorrent_day2.Rmd b/markdown/IonTorrent/Exercises_IonTorrent_day2.Rmd similarity index 100% rename from eLena_md/IonTorrent/Exercises_IonTorrent_day2.Rmd rename to markdown/IonTorrent/Exercises_IonTorrent_day2.Rmd diff --git a/eLena_md/IonTorrent/Images/phenodata_IonTorrent.png b/markdown/IonTorrent/Images/phenodata_IonTorrent.png similarity index 100% rename from eLena_md/IonTorrent/Images/phenodata_IonTorrent.png rename to markdown/IonTorrent/Images/phenodata_IonTorrent.png diff --git a/eLena_md/IonTorrent/Images/taxbar_IonTorrent.png b/markdown/IonTorrent/Images/taxbar_IonTorrent.png similarity index 100% rename from eLena_md/IonTorrent/Images/taxbar_IonTorrent.png rename to markdown/IonTorrent/Images/taxbar_IonTorrent.png diff --git a/eLena_md/exercises-d1/d1.Rmd b/markdown/MiSeq/Exercises_MiSeq_day1.Rmd similarity index 100% rename from eLena_md/exercises-d1/d1.Rmd rename to markdown/MiSeq/Exercises_MiSeq_day1.Rmd diff --git a/eLena_md/exercises-d2/d2.Rmd b/markdown/MiSeq/Exercises_MiSeq_day2.Rmd similarity index 100% rename from eLena_md/exercises-d2/d2.Rmd rename to markdown/MiSeq/Exercises_MiSeq_day2.Rmd diff --git a/eLena_md/exercises-d2/Images/pheno_layout.png b/markdown/MiSeq/Images/pheno_layout.png similarity index 100% rename from eLena_md/exercises-d2/Images/pheno_layout.png rename to markdown/MiSeq/Images/pheno_layout.png diff --git a/eLena_md/exercises-d2/Images/taxbar.png b/markdown/MiSeq/Images/taxbar.png similarity index 100% rename from eLena_md/exercises-d2/Images/taxbar.png rename to markdown/MiSeq/Images/taxbar.png diff --git a/eLena_md/video-transcripts-d2/.Rhistory b/markdown/MiSeq/video-transcripts-d2/.Rhistory similarity index 100% rename from eLena_md/video-transcripts-d2/.Rhistory rename to markdown/MiSeq/video-transcripts-d2/.Rhistory diff --git a/eLena_md/video-transcripts-d2/videos-d2.Rmd b/markdown/MiSeq/video-transcripts-d2/videos-d2.Rmd similarity index 100% rename from eLena_md/video-transcripts-d2/videos-d2.Rmd rename to markdown/MiSeq/video-transcripts-d2/videos-d2.Rmd diff --git a/markdown/updating_instructions.txt b/markdown/updating_instructions.txt new file mode 100644 index 0000000..e3ed4e8 --- /dev/null +++ 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! +