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GDC Viewer

Installation and Setup

The installation assumes you are working on an Ubuntu or MacOS machine.

0. Install dependencies

Note: You may find it easier to use a node versioning tool to install Node. Two popular tools are n and nvm.

1. Install JBrowse

Clone the JBrowse repostitory. Don’t switch into the directory just yet.

git clone https://github.com/GMOD/jbrowse

We will use the placeholder <jbrowse-location> to refer to where JBrowse is installed on your computer. An example would be /Users/aduncan/Downloads/jbrowse.

2. Install GDC Plugin

Clone the GDC plugin and then copy the gdc-viewer subfolder into the JBrowse plugins directory.

git clone https://github.com/LincolnSteinLab/gdc-viewer.git
cp -R gdc-viewer/gdc-viewer <jbrowse-location>/plugins/gdc-viewer

Now add the ‘gdc-viewer’ plugin to the array of plugins in the <jbrowse-location>/jbrowse.conf.

[ plugins.gdc-viewer ]
location = <jbrowse-location>/plugins/gdc-viewer

In the same file, add the following to use the faceted track selector.

[trackSelector]
type = Faceted
displayColumns =
  + label
  + key
  + datatype
  + case
  + project
  + primarySite

Note that this will only show preloaded tracks as well as tracks you have added using the various dialogs. It does not dynamically create tracks based on what is available from the GDC.

3. Install Reference Sequence Data

Now setup the reference sequence used. GDC requires the GRCh38 Human reference files.

Create the data directory in <jbrowse-location>/data.

cd <jbrowse-location>
mkdir data
cd data

Download the GRCh38 .fa and .fa.fai files online. Two places you could find these files are:

  • https://s3.amazonaws.com/igv.org.genomes/genomes.json
  • http://bioinfo.hpc.cam.ac.uk/downloads/datasets/fasta/grch38/

Then put the following in <jbrowse-location>/data/tracks.conf (note files may be named something else).

refSeqs=hg38.fa.fai
  
[tracks.refseqs]
urlTemplate=hg38.fa

4. Adding new tracks (optional)

We have some basic example tracks in the data/tracks.conf file of the gdc-viewer repository.

You can also add new tracks by using the GDC dialog accessible within JBrowse. See the tracks page.

5. Build JBrowse

Run the following commands to build JBrowse and the GDC plugin.

Note that ./setup.sh may print some errors about volvox, but they can be ignored. It may also take a few minutes.

cd <jbrowse-location>
./setup.sh
yarn

5. Run JBrowse

Then run the following commands:

yarn watch
# open a new terminal tab/window
yarn start

JBrowse should now be running with the GDC Plugin working! See the yarn start command to determine the port that the plugin is using.