A Loopback/Ember/D3 framework to display and interactively navigate complex datasets.
Developed by
- AgriBio, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Victoria, Australia;
- CSIRO, Canberra, Australia.
Funded by the Grains Research Development Corporation (GRDC).
- Features
- Quick start (using docker)
- Setting up your own instance (without docker)
- Public genetic map references
NOTE: References for the genetic maps shown in the alignments on this page are available at the bottom of this page.
For a quick start without installing any of the dependencies you will need docker engine running on your system.
mkdir -p ~/mongodata \
&& docker run --name mongo --detach --volume ~/mongodata:/data/db --net=host mongo \
&& until $(curl --silent --fail --output /dev/null localhost:27017); do printf '.'; sleep 1; done \
&& docker run --name pretzel --detach --net=host plantinformaticscollaboration/pretzel:stable \
&& until $(curl --silent --fail --output /dev/null localhost:3000); do printf '.'; sleep 1; done \
&& docker logs pretzel
md mongodata
docker run --name mongo --detach --publish 27017:27017 --volume mongodata:/data/db mongo
docker run --name pretzel -e "DB_HOST=host.docker.internal" --publish 3000:3000 plantinformaticscollaboration/pretzel:stable
If everything has worked so far, you should be able to open http://localhost:3000 in a browser and see a landing page. You can create a user by signing up, then logging in with these details (by default, the user is created immediately without any extra verification).
Once your pretzel instance is running you may want to populate it with some data.
You can start by downloading and decompressing datasets (3 genetic maps) we have made available here. In your instance of Pretzel, navigate to the Upload tab on the left panel, select JSON and browse to the location where you extracted the content of the downloaded file. Select and submit each of the three JSON files in turn. Once submitted, the maps should be visible in the Explorer tab.
To upload multiple genomes along with feature definitions and aliases defining syntenic relationships between the features, you can
- Download the pre-computed data,
wget https://github.com/plantinformatics/pretzel-input-generator/releases/download/v1.0/pretzel-genomes-features-aliases-JSON.tar.gz
- Unpack
tar xzvf pretzel-genomes-features-aliases-JSON.tar.gz
- Follow the upload instructions
Install MongoDB using your distribution's package manager; for example, in Ubuntu:
sudo apt-get install mongodb
NPM is the package manager for Node.js and allows easy installation of the tools required by this project. You can install Node.js and NPM using your native distribution package manager; for example, in Ubuntu:
sudo apt-get install nodejs npm
Bower is a front-end package manager and depends on Node.js and NPM. Install it globally:
sudo npm install bower -g
Prerequisites : XCode : https://itunes.apple.com/us/app/xcode/id497799835 Homebrew : https://brew.sh
brew install node
brew install mongodb
npm install bower -g
The default location of the mongo database is /data/db; to place the data in e.g. your home directory :
cd ~/Applications/
mkdir Pretzel
export MONGO_DATA_DB=$HOME/Applications/Pretzel/data_db
mkdir $MONGO_DATA_DB
mongod --dbpath $MONGO_DATA_DB
Clone the Github repository:
git clone https://github.com/plantinformatics/pretzel.git
To setup and build the frontend and backend, and run the backend :
cd pretzel
npm run go
This sections describes steps of default build individually, as an alternative to npm run go.
To install the various plug-ins and add-ons required by the project, use NPM and Bower (for the Ember-specific dependencies):
# cd into Ember directory
cd pretzel/frontend
# Install Ember dependencies
npm install
bower install
# cd into backend directory
cd ../backend
# Install dependencies
npm install
Note that npm install in backend/ and frontend/ will install the Express.js and
Ember.js dependencies, including Express.js and Ember.js themselves, into those directories. For
example, ember is in frontend/node_modules/ember-cli/bin/.
The app is served by the Loopback backend and needs to be pre-compiled:
cd ../frontend
node_modules/ember-cli/bin/ember build --environment production
cd ..
The Loopback backend expects the compiled client in its client/ sub-directory. You can simply create a soft link:
ln -s ../frontend/dist backend/client
You should now be able to start the Loopback backend:
cd backend
EMAIL_VERIFY=NONE AUTH=ALL node server/server.js
Note that this runs the app without any authentication or security and is only suitable for local installs or internal networks. See below for details on setting up user accounts and authentication.
If everything has worked so far, you should be able to open http://localhost:3000 in a browser and see a landing page. If you started the backend with the above command, you can create a user by signing up, then logging in with these details (with EMAIL_VERIFY=NONE, the user is created immediately without any extra verification).
There are five example maps in the resources/ folder with simple dummy data. You can upload these by navigating to the Upload tab on the left panel, selecting JSON and browsing to the resources/ folder to select a map. Once submitted, the maps should be visible in the Explorer tab.
An alternative to the Upload tab is to use the command-line, e.g. for larger files :
export APIHOST=http://localhost:3000 source ~/Applications/Pretzel/pretzel/resources/tools/functions_prod.bash
While logged into Pretzel via the browser, use the Web Inspector to get the authentication token : From Ctrl-click : Inspect ...
Application : Storage : Cookies : http://localhost:3000 : Name : ember_simple_auth-session Copy/Paste the Value into a url decoder such as e.g. https://urldecode.org which will display the decoded parameters as e.g. : {"authenticated":{"authenticator":"authenticator:pretzel-local","token":"0uOnWyy08OGcDJbC9eRx5Ki73z2OYkqvrZqQTJmoAklmysU5CxtrYmrXUpcX8MOe","clientId":"5ba9c0870612bf19a6afed01"}} Copy/paste the token value and set it in the command-line environment using :
setToken "authentication-token-goes-here"
uploadData ~/Applications/Pretzel/pretzel-data/myMap.json
Wang, S., Wong, D., Forrest, K., Allen, A., Chao, S., Huang, B. E., Maccaferri, M., Salvi, S., Milner, S. G., Cattivelli, L., Mastrangelo, A. M., Whan, A., Stephen, S., Barker, G., Wieseke, R., Plieske, J., International Wheat Genome Sequencing Consortium, Lillemo, M., Mather, D., Appels, R., Dolferus, R., Brown-Guedira, G., Korol, A., Akhunova, A. R., Feuillet, C., Salse, J., Morgante, M., Pozniak, C., Luo, M.-C., Dvorak, J., Morell, M., Dubcovsky, J., Ganal, M., Tuberosa, R., Lawley, C., Mikoulitch, I., Cavanagh, C., Edwards, K. J., Hayden, M. and Akhunov, E. (2014), Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. Plant Biotechnol J, 12: 787–796. doi:10.1111/pbi.12183
Gardner, K. A., Wittern, L. M. and Mackay, I. J. (2016), A highly recombined, high-density, eight-founder wheat MAGIC map reveals extensive segregation distortion and genomic locations of introgression segments. Plant Biotechnol J, 14: 1406–1417. doi:10.1111/pbi.12504
Wen, W., He, Z., Gao, F., Liu, J., Jin, H., Zhai, S., Xia, X. (2017). A High-Density Consensus Map of Common Wheat Integrating Four Mapping Populations Scanned by the 90K SNP Array. Frontiers in Plant Science, 8, 1389. http://doi.org/10.3389/fpls.2017.01389