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Template:GMOD VM

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{{GMOD VM
|name=GMOD in the Cloud
|logo=GitcLogo.png
|intro= // introductory blurb about the VM
|download= // info on where to download the VM
|os= // operating system of VM
|chado v= // versions of these tools
|gbrowse v=
|jbrowse v=
|tripal v=
|webapollo v=
|postgres v=
|drupal v=
|demo= // url of public demo
|poster=
|getting started=
|urltmpl=
|extra info=
|phone home details=
}}


{{{name}}} is a GMOD virtual server equipped with a suite of preconfigured GMOD components, including a Chado database, GBrowse2, JBrowse, Tripal, and Apollo or WebApollo. Setting up a {{{name}}} instance is quick and easy; it even comes with demo data to explore if you do not have your own. If you are investigating GMOD for the first time, {{{name}}} provides an excellent way to assess GMOD components without having to do any installation; for longer-term uses, the virtual server can be kept running as long as required, and data can easily be moved when new versions of {{{name}}} are released.


What's in {{{name}}}

Chado logo

GBrowse logo

GBrowse_syn logo

JBrowse logo

Tripal logo

WebApollo logo


Where to find {{{name}}}

{{{download}}}

Important note: {{{name}}} includes a small script that sends an email to the GMOD developers to let them know that someone is using a {{{name}}} instance. GMOD uses this to track the popularity of virtual GMOD installations for grants and funding purposes. For more information, see the phoning home section below.


Getting Started

{{{name}}} is running on {{{os}}}. The virtual machine is split into two partitions, root and data. All user information should be kept in the data partition to make backup and updates easy.



Directory Structure

When you first log in to the virtual machine, you will be in the ubuntu user's home directory, /home/ubuntu, on the root partition of the machine. We recommend that any information that you want to save be kept in the data partition. There is a link to the data partition called dataHome, so you can easily change directories by running cd /home/ubuntu/dataHome or cd ~/dataHome. The dataHome directory contains a bashrc (bash shell configuration file) that is automatically executed when you log in, and any shell environment changes you want to make should be added to this file.

There are several other important directories that have been moved to the data partition. In all cases, the original files have been replaced by symlinks, so changes made to the files noted below are picked up as if the files were in their original locations. If you need other files moved to the data partition, please email the GMOD developers list so that we can incorporate the changes into future iterations of {{{name}}}.

/data/etc/gbrowse The config directory for GBrowse.
/data/etc/postgresql The config directory for PostgreSQL
/data/opt A good place to install any other software you want to use
/data/var/lib/gbrowse2 Other GBrowse files that might be modifed on your instance, including user session data and flat file databases.
/data/var/lib/postgresql Files for the PostgreSQL database
/data/var/www/.htaccess The htaccess file for the main Drupal site
/data/var/www/jbrowse/jbrowse_conf.json Config file for JBrowse
/data/var/www/jbrowse/data All of the data files needed for running JBrowse
/data/var/www/sites/default Site-specific files and directories for Drupal; modules and themes go here (though Tripal is in /var/www/sites/all)
/data/webapollo WebApollo data
/data/var/lib/tomcat7/webapps/WebApollo/config Config options for WebApollo
/data/usr/share/tomcat7/bin setenv.sh for tomcat; used to increase allocated memory for tomcat

Note that changes made to files in any other locations will be lost.

Updating from previous versions

Instances of {{{name}}} can be updated by replacing the data partition in the new instance with the data partition from the old instance. For more information, see the updating guide.

Phoning home

When a {{{name}}} server starts up for the first time, it sends an email to the GMOD developers with information about the instance. These data are kept private and are strictly for statistical purposes, primarily for funding and grant applications.

{{{phone home details}}}

Installed GMOD software

PostgreSQL

Database name: drupal

Username: drupal

See the Postgres database connection parameters in /var/www/sites/default/settings.php for more information.

There is also a Postgres user named ubuntu with superuser privileges. The Postgres search_path for this user is set to look in the Chado schema before the public schema; this account should be used for tools that interact with Chado (e.g. GBrowse, Tripal, and any command line tools from GMOD).


Drupal

Version:

Source: Drupal website

Installation dir: /var/www

Web URL: {{{urltmpl}}}/

When navigating with a web browser to the Apache document root (i.e., http://127.0.0.1/ or the IP address of your server), you will get the Drupal home page.

New modules can be added at /data/var/www/sites/default/modules and new themes can be added at /data/var/www/sites/default/themes.


Tripal

Version:

Source: Tripal svn

Installation dir: /var/www/sites/all/modules/tripal


Chado

Version:

Tripal was used to install the Chado database schema and load ontologies and a GFF file containing yeast genome annotations from SGD (source: http://downloads.yeastgenome.org/curation/chromosomal_feature/saccharomyces_cerevisiae.gff), as well as a sample GFF contig file output from MAKER for the Pythium ultimum (source: http://icebox.lbl.gov/webapollo/data/pyu_data.tgz).

The Chado software package is in the home directory, ~/sources/chado, and was used to install many utility scripts via the standard installation method for Perl modules (perl Makefile.PL; make; sudo make install). This checkout can be updated with "svn update" like the Tripal svn checkout.


GBrowse2

Version:

The configuration file for the Chado database is /data/etc/gbrowse2; config files for the demo data: yeast: 07.chado.conf; P. ultimum: pythium.conf.

GBrowse is configured to use fcgid, a web server add-on that helps speed up GBrowse. To use it, your GBrowse URLs should look like this:

   {{{urltmpl}}}/fgb2/gbrowse/yeast

If there are problems with fcgid, you can still use the non-accelerated GBrowse at

   {{{urltmpl}}}/cgi-bin/gb2/gbrowse/yeast


JBrowse

Version:

Source: JBrowse website

Installation dir: /var/www/jbrowse

Web URL: {{{urltmpl}}}/jbrowse

Configuration file (defines database connection parameters, tracks): ~/jbrowse.conf.

The Pythium dataset was created in a way similar to the JBrowse tutorial and using the configuration file ~/pythium-1.conf.

JBrowse was configured to have multiple datasets using the jbrowse_conf.json file as described in the JBrowse configuration guide. This file is at /data/var/www/jbrowse/jbrowse_conf.json.


WebApollo

Version:

WebApollo was installed per the directions on the WebApollo page. In addition to the admin user, a second user with limited permissions was created with username: "guest", password: "guest".

Check out the WebApollo setup instructions specific to the VM for help in setting up your data.