Add dockerfile

rename R script

Author: markdunning

Dockerfile

@@ -0,0 +1,13 @@
+
+FROM bioconductor/release_base
+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 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

index.html

@@ -47,13 +47,28 @@ <h3>
         </p>
 
         <h3>
-        <a id="software" class="anchor" href="#software" aria-hidden="true"><span class="octicon octicon-link"></span></a>Software Requirements.</h3>
+        <a id="software" class="anchor" href="#software" aria-hidden="true"><span class="octicon octicon-link"></span></a>How to Run the course.</h3>
         <p>
+        Download the materials from this repository and <a href="GeneticPracticalPackageInstall.R">install</a> the required R and Bioconductor packages
+        </p>
+
+      <h3>
+        <a id="docker" class="anchor" href="#docker" aria-hidden="true"><span class="octicon octicon-link"></span></a>Using Docker.</h3>
+       <p>
+         
+         <pre class="input"><code>docker run -p 8787:8787 markdunning/ngs-in-bioc</code></pre>
+
+       </p>
+            
+
+ 
         </p>
 
         <h3>
         <a id="data" class="anchor" href="#data" aria-hidden="true"><span class="octicon octicon-link"></span></a>Example Data.</h3>
         <p>
+        An exampleData folder is required to run the practicals sucessfully. This folder can be downloaded from <a href="https://app.box.com/s/ntjkjn3vb4jkvy6kq664">https://app.box.com/s/ntjkjn3vb4jkvy6kq664.</a> Once downloaded and unzipped, the folder should be placed inside the Practicals directory
+        
         </p>