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fixed merge conflict
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domonik committed Apr 8, 2024
2 parents 5fe83f2 + 241543b commit e5933f1
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9 changes: 9 additions & 0 deletions .github/envs/environment.yml
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name: rmarkdown-env
channels:
- conda-forge
- defaults
dependencies:
- r-rmarkdown
- pandoc
- r-flextable
- r-officer
58 changes: 58 additions & 0 deletions .github/workflows/build-pages.yml
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name: build-github-pages
env:
GITHUB_ACTOR: BackofenLab
GITHUB_REPOSITORY: BackofenLab/V_RNA-pages
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

on:
push:
branches:
- main

# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:

# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
permissions:
contents: write
pages: write
id-token: write

jobs:
build_rmarkdown_job:
runs-on: ubuntu-latest
steps:
- name: Get prerequisites and clone repository
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: |
set -x
sudo apt-get update
sudo apt-get install -y git
git clone "https://token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" .
shell: bash

- name: create environment with mamba
uses: conda-incubator/setup-miniconda@v2
with:
mamba-version: "*"
channels: conda-forge,defaults
auto-activate-base: false
activate-environment: rmarkdown-env
environment-file: .github/envs/environment.yml

- name: Render Rmd files
run: |
eval "$(conda shell.bash hook)"
conda activate rmarkdown-env
Rscript -e "rmarkdown::render_site()"
- name: Upload artifact
uses: actions/upload-pages-artifact@v2
with:
# Upload entire repository
path: 'docs/'

- name: Deploy to GitHub Pages
id: deployment
uses: actions/deploy-pages@v2
3 changes: 2 additions & 1 deletion .gitignore
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Expand Up @@ -2,4 +2,5 @@
.Rhistory
.RData
.Ruserdata
docs/
docs

2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -4,5 +4,5 @@ This repository caintains all the files necessary to compile the self-learning e

The current version of the page can be found here:

https://bioinformatics2-teaching.github.io/BioinformaticsII-pages/
https://backofenlab.github.io/BioinformaticsII-pages/

3 changes: 1 addition & 2 deletions _site.yml
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@@ -1,7 +1,7 @@
name: "BioinformaticsII"
output_dir: "docs"
author: "@CARD"
date: "SS2022"
date: "SS2024"
language: en
output:
html_document:
Expand All @@ -19,5 +19,4 @@ output:
in_header: "_tex/latex_commands.tex"
urlcolor: blue
linkcolor: blue
exclude: ["*.tex", "*.log"]

4 changes: 2 additions & 2 deletions exercise-sheet-6.Rmd
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Expand Up @@ -171,7 +171,7 @@ List all possible words for the first $k$-length word (AT) that have a score of

### 2c)

Scan the database for exact matches for the words from the question 3B.
Scan the database for exact matches for the words from the question 2B.

#### {.tabset}

Expand All @@ -187,7 +187,7 @@ Scan the database for exact matches for the words from the question 3B.

### 2d)

Extend the exact matches that you found in the question 3C to the left/right and report all MSPs with a score greater than $4$.
Extend the exact matches that you found in the question 2C to the left/right and report all MSPs with a score greater than $4$.

#### {.tabset}

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