EpiDenovo

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What is EpiDenovo?

EpiDenovo is a database for annotation of the associations between embryonic epigenomes and DNMs in developmental disorders, including several neuropsychiatric disorders and congenital heart disease. EpiDenovo provides an easy-to-use web interface allowing users rapidly to find the epigenetic signatures of DNMs and the expression patterns of the genes that they regulate during embryonic development. In summary, EpiDenovo is a useful resource for selecting candidate genes for further functional studies in embryonic development of human and mouse, and for investigating DNMs causing or underlying developmental disorders of human.

About JBrowse

Installing JBrowse

Users of JBrowse should get it from the main JBrowse site at http://jbrowse.org/install.

Unless you intend to work on the JBrowse code itself, or develop a JBrowse plugin, stop reading now and go to http://jbrowse.org/install.

About running from a git clone

Only developers should run JBrowse from a git repository. For one reason, the development version has a much, much slower initial load time than the built release zipfiles. Also, since the master branch code is ''in development'' for the next JBrowse release, it often (usually?) contains bad bugs, much more so than the official releases put up on JBrowse.org.

Setting up a development environment

Make sure you have a web server installed on your development machine. Any web server will do.

cd /my/dev/webserver/root;
git clone --recursive git@github.com:YOURACCOUNT/jbrowse.git
cd jbrowse
./setup.sh
# and now point your browser to
#   http://localhost/jbrowse/index.html?data=sample_data/json/volvox
# and you should see the volvox example data

Then you can simply edit files and your changes will be available in the browser (i.e. no build step is required)

You can also optionally run build steps to create the minimized codebase

make -f build/Makefile release

To build the Electron app, run the following

npm install -g electron-packager
make -f build/Makefile release-electron-all

To run the Electron app in debug mode run the following

npm install
npm start

Running the developer test suites

Server-side Perl

Tests for the server-side Perl code. You must have the JBrowse Perl module prerequisites installed for them to work. Run with:

prove -Isrc/perl5 -lr tests

Client-side Unit Tests

Point your browser at http://my.dev.machine/jbrowse/tests/js_tests/index.html

You can also run them from phantomJS using

phantomjs tests/js_tests/run-jasmine.js http://my.dev.machine/jbrowse/tests/js_tests/index.html

Client-side Integration Tests

Integration tests for the client-side app. You need to have Python eggs for selenium and nose installed. Run the tests with:

JBROWSE_URL='http://localhost/jbrowse/index.html' nosetests

Cutting a JBrowse release

0. Create a directory and clone the repo: git clone --recursive https://github.com/GMOD/jbrowse.git Then for 1.12.1, git checkout tags/1.12.1-release (because it lives in a branch that is not master)

1. Edit the JBrowse package.json file and change 'version' to the version you are releasing. Don't commit this change to the repository, it should stay as dev in git so that it shows up in analytics as a development version.

2. Build the release packages: make -f build/Makefile release. The files produced during the build should not be committed to the repository either. There is also make -f build/Makefile release-notest for releases that don't need perl tests to be run. NOTE: you may need to use the command ulimit -n 1000 to avoid "spawn EMFILE" build errors.

3. Make a tag in the repository for the release, named, e.g. 1.6.3-release.

4. scp the release .zip files (min and full) to jbrowse.org.

5. Add them to the Wordpress Downloads list so that we can track how many times they are downloaded.

6. Write a blog post announcing the release. The release-notes.html file made during the build might be useful for this.

7. Update the "Install" page on the site to point to the newest release.

8. Update the latest-release code checkout on the site, which the "Latest Release" demo on the jbrowse.org points to, to be an unzipped-and-set-up copy of the latest release.

9. Write an email announcing the release, sending to gmod-ajax, jbrowse-dev. If it is a major release, add gmod-announce and make a GMOD news item.

As you can tell, this process could really use some more streamlining and automation.