- 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.
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.
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.
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 [email protected]: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
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
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
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
-
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)
-
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 asdev
in git so that it shows up in analytics as a development version. -
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 alsomake -f build/Makefile release-notest
for releases that don't need perl tests to be run. NOTE: you may need to use the commandulimit -n 1000
to avoid "spawn EMFILE" build errors. -
Make a tag in the repository for the release, named, e.g.
1.6.3-release
. -
scp
the release .zip files (min and full) to jbrowse.org. -
Add them to the Wordpress Downloads list so that we can track how many times they are downloaded.
-
Write a blog post announcing the release. The
release-notes.html
file made during the build might be useful for this. -
Update the "Install" page on the site to point to the newest release.
-
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.
-
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.