Configuration and miscellaneous support files for the AIP
project JBrowse
installation
For the AIP
project, please follow the steps outlined below for the setup and installation of the app:
### server: columbia
$ cd /opt/www/araport/htdocs
### clone the jbrowse-contrib repo
### remember to clone `--recursive` to get the submodule as well
### submodule `jbrowse-latest-release` points to latest release (https://github.com/GMOD/jbrowse/releases)
$ git clone --recursive https://github.com/Arabidopsis-Information-Portal/jbrowse-contrib.git .
### make a symlink and change into the release directory
### set up jbrowse by running the `setup.sh` script
$ ln -sf jbrowse-latest-release jbrowse
$ cd jbrowse
$ ./setup.sh
Point the web browser to http://araport-dev.jcvi.org/jbrowse to check that the app is functioning properly.
Before data can be loaded into JBrowse
, please following the instructions for setting up the data area from here: araport-contrib
Once the JBrowse
setup has completed successfully and data has been downloaded to the right location, refer to the following steps to load data:
### server: columbia
$ cd /opt/www/araport/htdocs/jbrowse
### create symlink to shared data area
$ ln -sf ../../data/jbrowse data
### copy config file(s), modified css/html and loading script to JBrowse installation directory
$ cp ../jbrowse-contrib/jbrowse-load.sh .
### run the loading script
$ ./jbrowse-load.sh > jbrowse-load.log 2> jbrowse-load.err
### after loading, replace the trackList.json config with the customized copy from the repo
$ cp ../jbrowse-contrib/data/json/arabiodopsis/trackList.json data/json/arabidopsis/trackList.json
This involves making use of a command line mechanism to push the app from dev --> test.
### prepare to push from dev --> test
### edit `tarinclude` file which lists relative paths to code that needs to be migrated
### Example line(s) in `tarinclude`:
./htdocs/jbrowse-latest-release
./htdocs/jbrowse
$ cd /opt/www/araport
$ vim tarinclude
### invoke push from dev --> test, this step only copies the app code
### data area is already shared between the dev and test servers
$ make
Point the web browser to http://araport-test.jcvi.org/jbrowse to check that the app is functioning properly.
This mechanism is regulated by rdist
, a remote file distribution client, which is controlled by a configuration file, called a distfile
.
### prepare to synch test with prod
### to check the areas that are set up to be synched, invoke the following command:
$ cd /opt/www/araport
$ make getdistfile
### this will retrieve a file called `distfile.araport`
### contains a list of directories to be mirrored (and a list of excluded directories as well)
### synch the application
$ make test2pro
### synch the data (if this is the first time, process will take a while: ~0.5 hrs)
$ make test2pro_data
Once the synch is complete, point the web browser to http://apps.araport.org/jbrowse to check that the app is functioning properly.