Difference between revisions of "Template:GMOD VM"

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m (More tinkerings and updates)
m (More tinkering)
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<noinclude>
 
<noinclude>
 +
<pre>
 
{{GMOD VM
 
{{GMOD VM
 
|name=GMOD in the Cloud
 
|name=GMOD in the Cloud
 
|logo=GitcLogo.png
 
|logo=GitcLogo.png
−
|catchy phrase=What's in the Cloud?
+
|intro= // introductory blurb about the VM
−
|chado v=
+
|download= // info on where to download the VM
 +
|os= // operating system of VM
 +
|chado v= // versions of these tools
 
|gbrowse v=
 
|gbrowse v=
 
|jbrowse v=
 
|jbrowse v=
Line 11: Line 14:
 
|postgres v=
 
|postgres v=
 
|drupal v=
 
|drupal v=
 +
|demo= // url of public demo
 
|poster=
 
|poster=
−
|tutorial=
+
|getting started=
 
|urltmpl=
 
|urltmpl=
 
|extras=
 
|extras=
 +
|phone home details=
 
}}
 
}}
 +
</pre>
 +
<!-- edit Template:GMOD AMI Info ( http://gmod.org/mediawiki/index.php?title=Template:GMOD_AMI_Info&action=edit ) to update the current GMOD in the Cloud info -->
 +
Current GMOD in the Cloud instance:
 +
{{Template:GMOD AMI Info}}
 +
  
 
</noinclude>
 
</noinclude>
 
{{#if: {{{logo|}}} | [[File:{{{logo}}}|right|400px|{{{name}}}]]|}}
 
{{#if: {{{logo|}}} | [[File:{{{logo}}}|right|400px|{{{name}}}]]|}}
−
{{{name}}} is a 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 possible tools, {{{name}}} provides an excellent way to assess GMOD components without having to do any installation, and the virtual server can be kept running as long as you need it.
+
{{{name}}} is a 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.
  
−
=={{{catchy phrase}}}==
+
{{#if:{{{intro|}}}|{{{intro}}}|}}
 +
{{#if: {{{demo|}}} |
 +
 
 +
[{{{demo}}} Visit the {{{name}}} demo server]
 +
 
 +
}}
 +
==What's in {{{name}}}==
 
{{#if: {{{poster|}}} | [[File:{{{poster}}}|right|300px|{{{name}}} poster]]|}}
 
{{#if: {{{poster|}}} | [[File:{{{poster}}}|right|300px|{{{name}}} poster]]|}}
  
Line 37: Line 53:
  
  
−
===Where is the Cloud?===
+
==Where to find {{{name}}}==
  
−
<!-- edit Template:GMOD AMI Info ( http://gmod.org/mediawiki/index.php?title=Template:GMOD_AMI_Info&action=edit ) to update the current GMOD in the Cloud info -->
+
{{{download}}}
−
Current GMOD in the Cloud instance:
+
−
{{Template:GMOD AMI Info}}
+
  
−
The virtual machine has a separate data partition to make backup and updates easy.
+
''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 [[{{PAGENAME}}#Phoning home|the phoning home section]] below.
  
−
Versions 1.1-1.3 of GMOD in the Cloud are compatible with [[Apollo]]; version 2.0 onwards contain [[WebApollo]].
+
{{{extra info}}}
  
−
''Important note:'' Starting with the 2.0 release of GMOD in the Cloud, the AMI "[[Cloud#Phoning_home|phones home]]" when started as an instance; that is, it sends an email to the developers to let them know that someone is using it.  For more information see below.
+
==Getting Started==
  
−
{{{extra info}}}
+
{{{name}}} is running on {{{os}}}. The virtual machine is split into two partitions, <code>root</code> and <code>data</code>. All user information should be kept in the <code>data</code> partition to make backup and updates easy.
−
===Tutorial===
+
  
−
There is a GMOD-centric [[GMOD_Cloud_Tutorial|tutorial for getting started with GMOD in the Cloud]].
+
{{#if:{{{getting started|}}} |
 +
{{{getting started}}}
 +
}}
  
−
===Directory structure===
 
  
−
When you log into your ... , you will be in the ubuntu user's home directory, /home/ubuntu, which is part of the root partition of the machine, and so, if you save anything in this directory, it will be deleted when you move to a new version of the GMOD Cloud. To save items from one machine to the next, it must be saved on your EBS partition, and to make that easier from the home directory, we've put in a link to the /data partition in the home directory named "dataHome", so you can "cd /home/ubuntu/dataHome" or "cd ~/dataHome" to save files in a convenient spot relative to your home directory. Already in this dataHome directory is a file called "bashrc" which is automatically included in your .bashrc when you log in, so if you have changes you'd like to make to your shell environment, you can add those changes here.
+
===Directory Structure==
  
−
There are several other directories that are on the /data partition so they will be saved when you go to a new instance as well. These are:
+
When you first log in to the virtual machine, you will be in the ''ubuntu'' user's home directory, <code>/home/ubuntu</code>, on the <code>root</code> partition of the machine. We recommend that any information that you want to save be kept in the <code>data</code> partition. There is a link to the <code>data</code> partition called <code>dataHome</code>, so you can easily change directories by running <code>cd /home/ubuntu/dataHome</code> or <code>cd ~/dataHome</code>. The <code>dataHome</code> directory contains a <code>bashrc</code> ([http://en.wikipedia.org/wiki/Bash_(Unix_shell)‎ 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 <code>data</code> 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 <code>data</code> partition, please [mailto:gmod-devel@lists.sourceforge.net email the GMOD developers list] so that we can incorporate the changes into future iterations of {{{name}}}.
  
 
{| class="wikitable"
 
{| class="wikitable"
Line 99: Line 115:
 
|}
 
|}
  
−
In all instances, the original files and directories where moved to the /data partition and replaced with symlinks to their new locations. Note that changes made to files in any other locations will be lost. If you find that you must have other files or directories saved, please send an email to gmod-devel@lists.sourceforge.net to request that symlinks be added to future releases.
+
Note that changes made to files in any other locations will be lost.
  
 
====Updating from previous versions====
 
====Updating from previous versions====
  
−
Instances of GMOD in the Cloud starting from 2.0 can be updated by replacing the /data partition in the new instance with the old /data partition (the one containing your data). For more information on how to do that, see the [[Cloud/Updating|Updating page]].
+
Instances of {{{name}}} can be updated by replacing the <code>data</code> partition in the new instance with the <code>data</code> partition from the old instance. For more information, see the [[{{PAGENAME}}/Updating|updating guide]].
 +
 
  
 
===Installed GMOD software===
 
===Installed GMOD software===
Line 109: Line 126:
 
====PostgreSQL====
 
====PostgreSQL====
  
−
Version:
+
The [[Postgres]] database name is '''drupal''', and the primary user for that database is also '''drupal'''. See the database connection parameters in <code>/var/www/sites/default/settings.php</code> for more information.
  
−
Source:
+
There is also a Postgres user named '''ubuntu''' with superuser privileges. The Postgres <code>search_path</code> 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).
  
−
The [[postgres]] database name is "drupal", and the primary user for that database is also called drupal.  See the database connection parameters in /var/www/sites/default/settings.php for more information.  There is also a postgres account named ubuntu (the same as the login shell user name) that has superuser privileges.  This account has its postgres "search_path" set so that it looks in the Chado schema before the public schema, and so this account should be used when using tools that are intended to interact with Chado (like GBrowse, Tripal, and any command line tools from GMOD).
 
  
 
====Drupal====
 
====Drupal====
Line 119: Line 135:
 
Version: {{{drupal v|}}}
 
Version: {{{drupal v|}}}
  
−
Source: http://drupal.org
+
Source: [http://drupal.org Drupal website]
  
 
Installation dir: <code>/var/www</code>
 
Installation dir: <code>/var/www</code>
 +
 +
Web URL: {{{urltmpl}}}
  
 
When navigating with a web browser to the Apache document root (i.e., http://127.0.0.1/ or whatever IP address your server is given), you will get the Drupal home page.
 
When navigating with a web browser to the Apache document root (i.e., http://127.0.0.1/ or whatever IP address your server is given), you will get the Drupal home page.
  
 
New modules can be added at <code>/data/var/www/sites/default/modules</code> and new themes can be added at <code>/data/var/www/sites/default/themes</code>.
 
New modules can be added at <code>/data/var/www/sites/default/modules</code> and new themes can be added at <code>/data/var/www/sites/default/themes</code>.
 +
  
 
====Tripal====
 
====Tripal====
Line 138: Line 157:
 
====Chado====
 
====Chado====
  
−
Tripal was used to install the Chado {{{chado v|}}} schema and load ontologies and
+
Version: {{{chado v|}}}
−
a GFF file containing yeast genome annotations from SGD, downloaded from
+
−
yeastgenome.org:
+
  
−
  http://downloads.yeastgenome.org/curation/chromosomal_feature/saccharomyces_cerevisiae.gff
+
Tripal was used to install the Chado {{{chado v|}}} 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 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 http://icebox.lbl.gov/webapollo/data/pyu_data.tgz].
  
−
as well as a sample GFF contig file output from [[MAKER]] for the ''Pythium ultimum''. It was downloaded from
+
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 (<code>perl Makefile.PL; make; sudo make install</code>). This checkout can be updated with "svn update" like the Tripal svn checkout.
  
−
  http://icebox.lbl.gov/webapollo/data/pyu_data.tgz
 
  
 
====GBrowse2====
 
====GBrowse2====
  
−
The version of [[GBrowse]]2 that is installed on this machine is {{{gbrowse v|}}}.  The configuration file for the Chado database is /data/etc/gbrowse2  and the yeast configuration file is 07.chado.conf, and for ''P. ultimum'' it is pythium.conf.
+
Version: {{{gbrowse v|}}}
  
−
GBrowse is configured to use fcgid, a web server "add on" that helps speed up GBrowse.  To use it, use URLs that look like this: {{{urltmpl}}}/fgb2/gbrowse/yeast, and if there are problems with fcgid, you can still use the non-accelerated GBrowse at {{{urltmpl}}}/cgi-bin/gb2/gbrowse/yeast.
+
The configuration file for the Chado database is /data/etc/gbrowse2; config files for the demo data: yeast: <code>07.chado.conf</code>; ''P. ultimum'': <code>pythium.conf</code>.
  
−
====JBrowse====
+
GBrowse is configured to use fcgid, a web server add-on that helps speed up GBrowse. To use it, use URLs that look like this:
  
−
[[JBrowse]] {{{jbrowse v|}}} was installed from a zip file obtained from http://jbrowse.org/ and is installed in
+
    {{{urltmpl}}}/fgb2/gbrowse/yeast
−
<code>/var/www/jbrowse</code>, so that navigating to {{{urltmpl}}}/jbrowse
+
−
will give the page.  The configuration file for defining database connection
+
−
parameters and created tracks is in the home directory: <code>~/jbrowse.conf</code>.
+
  
−
The Pythium dataset was created in a way similar to the [[JBrowse_Tutorial_2012|JBrowse tutorial]] and using the configuration file <code>~/pythium-1.conf</code>.
+
If there are problems with fcgid, you can still use the non-accelerated GBrowse at
  
−
JBrowse was configured to have multiple datasets using the jbrowse_conf.json file as described in the [[JBrowse_Configuration_Guide#Dataset_Selector]].  This file is the data partition at <code>/data/var/www/jbrowse/jbrowse_conf.json</code>.
+
    {{{urltmpl}}}/cgi-bin/gb2/gbrowse/yeast
  
−
====Chado====
 
  
−
While the [[Chado]] schema was installed by Tripal, 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 (<code>perl Makefile.PL; make; sudo make install</code>).  This checkout can be updated with "svn update" like the Tripal svn checkout.
+
====JBrowse====
  
−
====WebApollo====
+
Version: {{{jbrowse v|}}}
  
−
WebApollo was installed essentially per the directions on the [[WebApollo]] page.  In addition to creating an admin user, another user with limited permissions was also created.  That user is called "guest" and has "guest" as the password.
+
Source: [http://jbrowse.org JBrowse website]
  
−
===Phoning home===
+
Installation dir: <code>/var/www/jbrowse</code>
  
−
Starting with the 1.4 release of GMOD in the Cloud, by default when an instance starts up for the first time, the instance sends an email to the GMOD developers letting them know that an instance has started, what the ID of the AMI was that it was started from, the size of the instance and what its public IP address is. This information will only be used for statistical purposes, primarily for applying for grants. The behavior can be modified in two ways:
+
Web URL: {{{urltmpl}}}/jbrowse
  
−
====Turning phone home off====
+
Configuration file (defines database connection parameters, tracks): <code>~/jbrowse.conf</code>.
  
−
In order to suppress sending the registration email, you can provide user data when initializing the instance to turn it off. Put this in the user data box:
+
The Pythium dataset was created in a way similar to the [[JBrowse_Tutorial_2012|JBrowse tutorial]] and using the configuration file <code>~/pythium-1.conf</code>.
  
−
  NoCallHome : 1
+
JBrowse was configured to have multiple datasets using the jbrowse_conf.json file as described in the [[JBrowse_Configuration_Guide#Dataset_Selector]]. This file is at <code>/data/var/www/jbrowse/jbrowse_conf.json</code>.
  
−
====Providing addition details====
 
  
−
You can also provide additional details when the instance sends the registration email. You can provide a contact email, name of your organization and the names of the organisms that you intend to use GMOD in the Cloud for.  To provide this information, set these items in the userdata box:
+
====WebApollo====
 +
 
 +
Version: {{{webapollo v|}}}
 +
 
 +
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".
 +
 
 +
 
 +
===Phoning home===
  
−
  email : your@emailaddress.com
+
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.
−
  org : name of your organization
+
−
  organism : name of the organism
+
  
−
The additional information will help us when it comes time to apply for grants.
+
{{{phone home details}}}

Revision as of 01:12, 22 November 2013

{{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=
|extras=
|phone home details=
}}

Current GMOD in the Cloud instance:

  • Amazon AMI ID: ami-a9d7f9c0 (in the US East-Virgina zone);
  • Name: GMOD in the Cloud 2.05

(as of December 16, 2013)



{{{name}}} is a 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.

{{{extra info}}}

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.


Installed GMOD software

PostgreSQL

The Postgres database name is drupal, and the primary user for that database is also drupal. See the 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 whatever IP address your server is given), 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

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, use URLs that 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#Dataset_Selector. 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".


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}}}

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