create links in html page

Author: markdunning

Dockerfile

@@ -5,9 +5,9 @@ MAINTAINER Mark Dunning<[email protected]>
 
 RUN apt-get update && apt-get install -y git
 ###Get repository of the course. Install data and R packages
-RUN git clone https://github.com/bioinformatics-core-shared-training/ngs-in-bioc.git /home/rstudio/cruk-bioinf-training 
-WORKDIR /home/rstudio/cruk-bioinf-training 
+RUN git clone https://github.com/bioinformatics-core-shared-training/ngs-in-bioc.git /home/rstudio/
+WORKDIR /home/rstudio
 RUN wget https://www.dropbox.com/s/ve6o68hkbthe3lo/exampleData.zip
 RUN unzip exampleData.zip
 RUN R -f installBioCPkgs.R
-RUN rm -r images javascripts stylesheets params.json index.html
+RUN rm -r images javascripts stylesheets params.json index.html exampleData.zip

index.html

@@ -77,26 +77,35 @@ <h3>
   <a id="day1" class="anchor" href="#day1" aria-hidden="true"><span class="octicon octicon-link"></span></a>Day One.</h3>
   <p>
 
-
-
+  <li><a href="Lectures/Lect1_HTSeq_Introduction_Sept2014.pdf">Introduction to NGS Sequencing</a></li>
+  <li><a href="Lectures/Lect2-StringsAndRanges.pdf">StringsAndRanges</a></li>
+  <li><a href="Practicals/1. StringsAndRanges-Prac.pdf">StringsAndRanges Practical</a></li>
+  <li><a href="Lectures/Lect3-CopyNumber_HT.pdf">Copy Number analysis</a></li>
+  <li><a href="Practicals/2.CopyNumber_DNASEQ-Prac.pdf">Copy Number analysis (Practical)</a></li>
+  <li><a href="Lectures/Lect4-DesignStatistics_HTSeq.pdf">Linear Models and Experimental Design</a></li>
 </p>
 
 
   <h3>
   <a id="day1" class="anchor" href="#day2" aria-hidden="true"><span class="octicon octicon-link"></span></a>Day Two.</h3>
   <p>
-
-
-
-  </p>
+  <li><a href="Lectures/Lect5_RNAseq_Sept2014.pdf">Introduction to RNA Sequencing</a></li>
+  <li><a href="Practicals/3. RNAseq-practical.pdf">RNA-seq Practical</a></li>
+  <li><a href="Lectures/Lect6a_Introduction_to_Annotation.pdf">Introduction to Genome Annotation</a></li>
+  <li><a href="Lectures/Lect6b_GenomeAnnotation.pdf">Genome Annotation in Bioconductor</a></li>
+  <li><a href="Practicals/4.Annotation-and-Visualisation.pdf">Genome Annotation Practical</a></li>
+</p>
 
 
   <h3>
   <a id="day1" class="anchor" href="#day3" aria-hidden="true"><span class="octicon octicon-link"></span></a>Day Three.</h3>
   <p>
-
-
-
+     <li><a href="Lectures/Lect7a_ChIP-Seq_Data_Analysis.pdf">Introduction to ChIP-Seq</a></li>
+     <li><a href="Lectures/Lect7b_ChIP-Seq Data Analysis.pdf">Analysis of ChIP-Seq</a></li>
+     <li><a href="Practicals/ChIP-Seq_Practical_1.pdf">ChIP-Seq Practical 1</a></li>
+     <li><a href="Lectures/Lect7c_ChIP-Seq DifferentialBinding.pdf">Differential Binding</a></li>
+     <li><a href="Practicals/ChIP-Seq_Practical_2.pdf">ChIP-Seq Practical 2</a></li>
+     <li><a href="Practicals/ChIP-Seq_Practical_3.pdf">ChIP-Seq Practical 3</a></li>
   </p>
 
         </section>