initial commit

.github/envs/environment.yml

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+name: rmarkdown-env
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - r-rmarkdown
+  - pandoc
+  - r-flextable
+  - r-officer

.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

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+docs
+

README.md

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+# BioinformaticsII-pages
+
+This repository caintains all the files necessary to compile the self-learning exercise sheets for the "Bioinformatics II" course of the bioinformatics group at the university of Freiburg.
+
+The current version of the page can be found here:
+
+https://backofenlab.github.io/BioinformaticsII-pages/
+

_navbar.html

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+<div class="navbar navbar-default  navbar-fixed-top" role="navigation">
+  <div style="background:white">
+  </div>
+  <div class="container">
+    <div class="navbar-header">
+      <!-- NOTE: add "navbar-inverse" class for an alternate navbar background -->
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <a class="navbar-brand navbar-img" href="#">
+        <div class="d-flex align-items-center h-25">
+          <img src="figures/bioinf-fr-logo-blau.svg" class="d-flex align-items-center" alt="">
+        </div>
+
+      </a>
+              <a class="navbar-brand">Optimierung</a>
+
+    </div>
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li><a href="exercise-sheet-1.html">ES 1</a></li>
+
+
+        <!--<li><a href="exercise-sheet-10.html">Sheet 10</a></li>-->
+      </ul>
+      <ul class="nav navbar-nav navbar-right">
+        <li><a href="http://www.bioinf.uni-freiburg.de/index.html?en2">Contact</a></li>
+      </ul>
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->

_site.yml

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+name: "BioinformaticsII"
+output_dir: "docs"
+author: "@CARD"
+date: "SS2024"
+language: en
+output:
+  html_document:
+    self_contained: no # ensure no html embedding of plots etc
+    toc: true
+    toc_depth: 3
+    toc_float:
+      collapsed: false
+    theme: "cosmo"
+    css: "bioinf-style.css"
+    includes:
+        in_header: header.html
+        after_body: "assets/html/removeSolution.html"
+urlcolor: blue
+linkcolor: blue
+

_tex/latex_commands.log

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+This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex 2021.9.27)  17 MAR 2022 11:47
+entering extended mode
+ restricted \write18 enabled.
+ %&-line parsing enabled.
+**latex_commands.tex
+(./latex_commands.tex
+LaTeX2e <2020-02-02> patch level 2
+L3 programming layer <2020-02-14>)
+! Emergency stop.
+<*> latex_commands.tex
+
+*** (job aborted, no legal \end found)
+
+
+Here is how much of TeX's memory you used:
+ 16 strings out of 481239
+ 417 string characters out of 5920377
+ 236561 words of memory out of 5000000
+ 15384 multiletter control sequences out of 15000+600000
+ 532338 words of font info for 24 fonts, out of 8000000 for 9000
+ 1141 hyphenation exceptions out of 8191
+ 12i,0n,15p,50b,8s stack positions out of 5000i,500n,10000p,200000b,80000s
+!  ==> Fatal error occurred, no output PDF file produced!

_tex/latex_commands.tex

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+\usepackage{amsmath}
+\usepackage{verbatim}
+\usepackage{easytable}
+\usepackage[linesnumbered,lined,boxed,commentsnumbered]{algorithm2e}
+
+\DeclareUnicodeCharacter{26A0}{!}
+\DeclareUnicodeCharacter{2685}{6}
+% environment for questions and answers
+\newenvironment{question}{}{}
+\newenvironment{answer}{}{}
+

assets/html/removeSolution.html

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+<script src="assets/js/restylePage.js"></script>
+<script src="assets/js/removeSolution.js"></script>