Difference between revisions of "Template:GMOD VM"
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 | ||
− | | | + | |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= | ||
− | | | + | |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 | + | {{{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. |
− | =={{{ | + | {{#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 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 [[{{PAGENAME}}#Phoning home|the phoning home section]] below. | |
− | + | {{{extra info}}} | |
− | + | ==Getting Started== | |
− | {{{ | + | {{{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. |
− | + | ||
− | + | {{#if:{{{getting started|}}} | | |
+ | {{{getting started}}} | ||
+ | }} | ||
− | |||
− | + | ===Directory Structure== | |
− | There are several other directories that | + | 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: | ||
|} | |} | ||
− | + | Note that changes made to files in any other locations will be lost. | |
====Updating from previous versions==== | ====Updating from previous versions==== | ||
− | Instances of | + | 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==== | ||
− | + | 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. | |
− | + | 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). | |
− | |||
====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==== | ||
− | + | Version: {{{chado v|}}} | |
− | + | ||
− | + | ||
− | + | 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]. | |
− | + | 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. | |
− | |||
====GBrowse2==== | ====GBrowse2==== | ||
− | + | Version: {{{gbrowse v|}}} | |
− | + | 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>. | |
− | + | 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: {{{jbrowse v|}}} | |
− | + | Source: [http://jbrowse.org JBrowse website] | |
− | + | Installation dir: <code>/var/www/jbrowse</code> | |
− | + | Web URL: {{{urltmpl}}}/jbrowse | |
− | + | Configuration file (defines database connection parameters, tracks): <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>. | |
− | + | 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>. | |
− | |||
− | + | ====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=== | ||
− | + | 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}}} |
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.
Contents
What's in {{{name}}}
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}}}