Cheaha - User contributions [en]

File:Jbasney-dissert-condensed.pdf

2012-06-29T20:01:58Z

Ppreddy@uab.edu:

File:15-09 Buetow.pdf

2012-06-21T16:48:18Z

Ppreddy@uab.edu:

GalaxyFAQ

2012-06-11T20:06:41Z

Ppreddy@uab.edu: /* When I hit Execute from Galaxy, does that mean the job is running on the cluster? */ Add information and steps involved in the run states of a job launched from galaxy web interface

__TOC__
FAQ for [[Galaxy]]

== Personal Galaxy ==

=== What does ''channel 3: open failed: connect failed: Connection refused'' mean? ===

This error shows up when attempting an ssh port forwarding from the galaxy server to the localhost. This error occurs due to port conflict on the server side. The port number mentioned during the execution of ''personalize.sh'' might already be taken up ie., a service might already be running at this port. Check the list of ports opened by doing a ''netstat -lpn |grep <port-number>''. If the result is not empty, run the ''personalize.sh'' script again with a higher port number and then ssh port forward with this new port number. On Unix/Linux systems, normal users can open ports starting from 1025 to 65535.

=== I've set up a Personal Galaxy, now what? ===

You could run jobs either from the command-line or from the galaxy web interface.
# Command-line - Run jobs in either [https://dev.uabgrid.uab.edu/wiki/GalaxyUsingToolWrappersFromCommandLine#Interactivemode interactive mode] or [https://dev.uabgrid.uab.edu/wiki/GalaxyUsingToolWrappersFromCommandLine#Non-interactivemode batch mode] on the SGE cluster.
# Web interface - Follow either the [[Galaxy_DNA-Seq_Tutorial|DNA-Seq]] or [[UAB_Galaxy_RNA_Seq_Step_by_Step_Tutorial|RNA-seq]] tutorials to run some NGS QC and manipulation jobs on the cluster from the galaxy web interface. The datasets related to these two tutorials can be downloaded from the [https://galaxy.uabgrid.uab.edu/ UAB Galaxy server] from its [https://galaxy.uabgrid.uab.edu/library shared data libraries.] NOTE: Access to UAB's galaxy server requires blazer-id authentication.

=== When I hit ''Execute'' from Galaxy, does that mean the job is running on the cluster? ===

Yes. Almost all ''Execute'' operations for the tools listed in the left-hand side of the galaxy web interface result in a running a ''qsub'' job on the cluster. Once you hit the ''Execute'' button, the job goes through a series of events such as:
# For the first few minutes after execute, you will see the watch icon next to the dataset in the History pane on the right hand side. This means that the job has been submitted to the queue and is in queue wait/hold state. Monitor this activity on the cluster by doing a ''qstat''.
# After a while, you will see a spinning icon next to the dataset. This means the job is running on the cluster.
# Once the spinning icon disappears, this means that the job is complete. You may perform any of the following actions to view your results:
## View the results in the data browser (middle pane) by clicking on the ''Eye'' icon in the History pane, to the right of your dataset.
## Click on the finished dataset itself. This displays a menu below the dataset in the History pane. The displayed options are to save, view details, run the job again, edit, annotate tags associated with the job.
### If you click on the ''info'' icon, you can view details on the job run like, the standard output, standard error and the actual file path on the cluster where your resulting datasets are located.

=== Where are the log files (stdout/stderr) for the job executed from Personal Galaxy? ===

Galaxy provides two ways in which you can access the job's stdout and stderr content.
:1. database - Galaxy stores the standard out and standard error in the database. The table which contains job's stdout and stderr is ''job'' and to view the same, use the following sql query
<pre>
sqlite> select tool_id,stdout,stderr from job where id=23;
tool_id stdout stderr
------------- ------------------------------------ ----------
fastq_trimmer 2913558 fastq reads were processed.
</pre>

:2. web interface - Galaxy web interface provides an html link to the job's stdout and stderr. This can be accessed by clicking on the tool panel's (the panel on the righthand side) info button for each tool -> Tool Standard Output / Tool Standard Error links.

:During the run of the job on SGE runner, the .o (stout) and .e (stderr) files are created in the directory specified by ''$file_path'' in universe_wsgi,ini. These .o and .e files are removed automatically, once the job is complete. To preserve these two files on the file system, run galaxy in debug mode ie., set ''debug = True'' in universe_wsgi.ini.

GalaxyFAQ

2012-06-11T19:49:33Z

Ppreddy@uab.edu: /* I've set up a Personal Galaxy, now what? */ add information and links on running jobs and tutorials to follow as the next step to installing personal galaxy

GalaxyFAQ

2012-06-11T19:33:27Z

Ppreddy@uab.edu: /* Where are the log files (stdout/stderr) for the job executed from Personal Galaxy? */ move text from new line to the list definition

GalaxyFAQ

2012-06-11T17:30:47Z

Ppreddy@uab.edu: /* Where are the log files (stdout/stderr) for the job executed from Personal Galaxy? */ explanation after personal investigations and response from psi galaxy-user uab galaxy-dev

GalaxyFAQ

2012-06-08T14:40:11Z

Ppreddy@uab.edu: turn sub heading to question

GalaxyFAQ

2012-06-07T19:01:56Z

Ppreddy@uab.edu: add 3 more questions

__TOC__
FAQ for [[Galaxy]]

== Personal Galaxy ==

=== Error: channel 3: open failed: connect failed: Connection refused ===

This error shows up when attempting an ssh port forwarding from the galaxy server to the localhost. This error occurs due to port conflict on the server side. The port number mentioned during the execution of ''personalize.sh'' might already be taken up ie., a service might already be running at this port. Check the list of ports opened by doing a ''netstat -lpn |grep <port-number>''. If the result is not empty, run the ''personalize.sh'' script again with a higher port number and then ssh port forward with this new port number. Usually in Unix/Linux systems, normal users can open ports starting from 1025 to 65535. However, some Unix/Linux systems have [http://en.wikipedia.org/wiki/Ephemeral_port Ephemeral port range] from 1025-5000. So, its safer to use a port number above 5000.

=== I've set up a Personal Galaxy, now what? ===

=== When I hit ''Execute'' from Galaxy, does that mean the job is running on the cluster? ===

=== Where are the log files (stdout/stderr) for the job executed from Personal Galaxy? ===

GalaxyFAQ

2012-06-07T17:47:49Z

Ppreddy@uab.edu: Fix sentence formation

GalaxyFAQ

2012-06-07T17:42:17Z

Ppreddy@uab.edu: add TOC macro

__TOC__
FAQ for [[Galaxy]]

== Personal Galaxy ==

=== Error: channel 3: open failed: connect failed: Connection refused ===

This error shows up when attempting an ssh port forwarding from the galaxy server to the localhost. This error occurs due to port conflict on the server side. The port number mentioned during the execution of ''personalize.sh'' might already be taken up ie., a service might already be running at this port. Check the list of ports opened by doing a ''netstat -lpn |grep <port-number>''. If the result is not empty, run the ''personalize.sh'' script again with a higher port number. In Unix/Linux systems, normal users can open ports starting from 1025 to 65535. However, some Unix/Linux systems have [http://en.wikipedia.org/wiki/Ephemeral_port Ephemeral port range] from 1025-5000. So, its safer to use a port number above 5000.

GalaxyFAQ

2012-06-07T17:41:06Z

Ppreddy@uab.edu: /* Error: channel 3: open failed: connect failed: Connection refused */

FAQ for [[Galaxy]]

== Personal Galaxy ==

=== Error: channel 3: open failed: connect failed: Connection refused ===

This error shows up when attempting an ssh port forwarding from the galaxy server to the localhost. This error occurs due to port conflict on the server side. The port number mentioned during the execution of ''personalize.sh'' might already be taken up ie., a service might already be running at this port. Check the list of ports opened by doing a ''netstat -lpn |grep <port-number>''. If the result is not empty, run the ''personalize.sh'' script again with a higher port number. In Unix/Linux systems, normal users can open ports starting from 1025 to 65535. However, some Unix/Linux systems have [http://en.wikipedia.org/wiki/Ephemeral_port Ephemeral port range] from 1025-5000. So, its safer to use a port number above 5000.

GalaxyFAQ

2012-06-07T17:40:34Z

Ppreddy@uab.edu: /* Error: channel 3: open failed: connect failed: Connection refused */

FAQ for [[Galaxy]]

== Personal Galaxy ==

=== Error: channel 3: open failed: connect failed: Connection refused ===

This error shows up when attempting an ssh port forwarding from the galaxy server to the localhost. This error occurs due to port conflict on the server side. The port number mentioned during the execution of ''personalize.sh'' might already be taken up ie., a service might already be running at this port. Check the list of ports opened by doing a ''netstat -lpn |grep <port-number>''. If the result is not empty, run the ''personalize.sh'' script again with a higher port number. In Unix/Linux systems, normal users can open ports starting from 1025 to 65535. However, some Unix/Linux systems have [[http://en.wikipedia.org/wiki/Ephemeral_port Ephemeral port range]] from 1025-5000. So, its safer to use a port number above 5000.

GalaxyFAQ

2012-06-07T17:38:29Z

Ppreddy@uab.edu: start GalaxyFAQ with first question on ssh port forwarding error

FAQ for [[Galaxy]]

== Personal Galaxy ==

=== Error: channel 3: open failed: connect failed: Connection refused ===

This error shows up when attempting an ssh port forwarding from the galaxy server to the localhost. This error occurs due to port conflict on the server side. The port number mentioned during the execution of ''personalize.sh'' might already be taken up ie., a service might already be running at this port. Check the list of ports opened by doing a ''netstat -lpn |grep <port-number>''. If the result is not empty, run the ''personalize.sh'' script again with a higher port number. In Unix/Linux systems, normal users can open ports starting from 1025 to 65535. However, some Unix/Linux systems have [[http://en.wikipedia.org/wiki/Ephemeral_port Ephemeral port range] from 1025-5000. So, its safer to use a port number above 5000.

Mediawiki

2012-01-25T21:38:15Z

Ppreddy@uab.edu: /* Interwiki Links */ correct syntax

__TOC__

== Overview ==

[http://www.mediawiki.org/wiki/MediaWiki Mediawiki] is a wiki software to enable communities to write documents collaboratively [http://en.wikipedia.org/wiki/Wiki#Characteristics]. Mediawiki, written in PHP, is what powers [http://www.wikipedia.org/ Wikipedia] and also [http://docs.uabgrid.uab.edu/wiki/Welcome UABgrid documentation]. The markup for Mediawiki is similar to other open-source wiki software like Trac, ie., it has WYSIWIG editing capabilities to translate formatting instructions to corresponding HTML tags.

For any questions on [http://docs.uabgrid.uab.edu UABgrid docs] or for having your own wiki space, please send an email to [mailto:support@vo.uabgrid.uab.edu support@vo.aubgrid.uab.edu].

== Users ==

Help on [http://www.mediawiki.org/wiki/Help:Editing_pages editing wikis] and [http://www.mediawiki.org/wiki/Help:Formatting formatting text] etc. on mediawiki can be found [http://www.mediawiki.org/wiki/Help:Contents here].

== Wiki Owners ==

=== Users and Groups Management ===
To view the current list of groups (and permissions for each group) or users for your wiki, go to
# '''Special pages''' link in the ''Toolbox'' section (left sidebar) of your wiki
# Click on '''User group rights''' (groups) or '''Users list''' (users)

Group permissions for the current mediawiki install on UABgrid is managed in the following manner:
# Click on '''Special pages''' link in the ''Toolbox'' section (left sidebar) of your wiki
# Click on '''User rights management''' link in the ''Users and rights'' section
# Type '''#<user-id>''' for eg., '''#3''' in the text box for the username. (this is because of [http://dev.uabgrid.uab.edu/ticket/183 limitations with the current mediawiki] install on docs)
# Check/uncheck the boxes to change groups for the user-id mentioned above

=== Interwiki Links ===
Mediawiki provides an easy way to point to non-wiki sites with URL substitution in the form of [http://www.mediawiki.org/wiki/Help:Links#Interwiki_links Interwiki links]. You can add/edit the current list of interwiki links for your wiki by going to
# '''Special pages''' link on the left sidebar
# Click on '''View and edit interwiki data''' in the ''Wiki data and tools section''

== Developers ==

To setup and develop for mediawiki on UABgrid, please see the [[MediawikiDev|page here]].

== References ==

: [http://www.mediawiki.org/wiki/MediaWiki Mediawiki]
: [http://download.wikimedia.org/mediawiki/1.16/mediawiki-1.16.0.tar.gz Download Mediawiki]
: [http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Mac_OS_X#Setting_up_MediaWiki Setting up Mediawiki]

Mediawiki

2012-01-25T21:25:37Z

Ppreddy@uab.edu: /* Wiki Owners */ add users, groups management and editing interwiki links

__TOC__

== Overview ==

[http://www.mediawiki.org/wiki/MediaWiki Mediawiki] is a wiki software to enable communities to write documents collaboratively [http://en.wikipedia.org/wiki/Wiki#Characteristics]. Mediawiki, written in PHP, is what powers [http://www.wikipedia.org/ Wikipedia] and also [http://docs.uabgrid.uab.edu/wiki/Welcome UABgrid documentation]. The markup for Mediawiki is similar to other open-source wiki software like Trac, ie., it has WYSIWIG editing capabilities to translate formatting instructions to corresponding HTML tags.

For any questions on [http://docs.uabgrid.uab.edu UABgrid docs] or for having your own wiki space, please send an email to [mailto:support@vo.uabgrid.uab.edu support@vo.aubgrid.uab.edu].

== Users ==

Help on [http://www.mediawiki.org/wiki/Help:Editing_pages editing wikis] and [http://www.mediawiki.org/wiki/Help:Formatting formatting text] etc. on mediawiki can be found [http://www.mediawiki.org/wiki/Help:Contents here].

== Wiki Owners ==

=== Users and Groups Management ===
To view the current list of groups (and permissions for each group) or users for your wiki, go to
# '''Special pages''' link in the ''Toolbox'' section (left sidebar) of your wiki
# Click on '''User group rights''' (groups) or '''Users list''' (users)

Group permissions for the current mediawiki install on UABgrid is managed in the following manner:
# Click on '''Special pages''' link in the ''Toolbox'' section (left sidebar) of your wiki
# Click on '''User rights management''' link in the ''Users and rights'' section
# Type '''#<user-id>''' for eg., '''#3''' in the text box for the username. (this is because of [http://dev.uabgrid.uab.edu/ticket/183 limitations with the current mediawiki] install on docs)
# Check/uncheck the boxes to change groups for the user-id mentioned above

=== Interwiki Links ===
Mediawiki provides an easy way to point to non-wiki sites with URL substitution in the form of [http://www.mediawiki.org/wiki/Help:Links#Interwiki_links Interwiki links]. You can add edit the current list of interwiki links for your wiki by going to
# '''Special pages''' link on the left sidebar
# Click on '''View and edit interwiki data''' in the ''Wiki data and tools section''

== Developers ==

To setup and develop for mediawiki on UABgrid, please see the [[MediawikiDev|page here]].

== References ==

: [http://www.mediawiki.org/wiki/MediaWiki Mediawiki]
: [http://download.wikimedia.org/mediawiki/1.16/mediawiki-1.16.0.tar.gz Download Mediawiki]
: [http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Mac_OS_X#Setting_up_MediaWiki Setting up Mediawiki]

Mediawiki

2012-01-25T21:17:51Z

Ppreddy@uab.edu: change End Users to Users and add Wiki Owners section with group management instrux

Mediawiki

2012-01-25T20:52:03Z

Ppreddy@uab.edu: /* End Users */ Modify text to point to mediawiki help pages

Mediawiki

2012-01-25T20:37:47Z

Ppreddy@uab.edu: /* Developers */ move developer content to MediawikiDev

MediawikiDev

2012-01-25T20:34:35Z

Ppreddy@uab.edu: copy developer content from Mediawiki

__TOC__
For developers interested in customizing Mediawiki (themes, plugins etc), an AMP (Apache, MySQL, PHP) stack is required. Recommended here, is one easy way to set up an AMP stack on Mac OS X with [http://docs.uabgrid.uab.edu/wiki/XAMPP XAMPP] developed by Apache Friends.

=== Mac OS X ===
==== XAMPP ====
:1. [http://docs.uabgrid.uab.edu/wiki/XAMPP Install and configure XAMPP for Mac].
:'''NOTE''': Mediawiki requires atleast PHP version of 5.3.2 or later. PHP - 5.3.1 version is incompatible with Mediawiki and this is the version which comes with the current stable releases of XAMPP.
:::So, for Mediawiki development, [http://www.apachefriends.org/en/xampp-beta.html '''use XAMPP beta'''].
:2. Start up xampp as root, either from xampp's control or from command line. This starts both Apache and mysql services.
<pre>
$ sudo /Applications/XAMPP/xamppfiles/xampp start
</pre>

==== Database ====

:1. Set up a database for mediawiki using xampp's '''phpmyadmin''' console. Go to http://localhost/phpmyadmin/ to open up phpmyadmin console
:2. Create a database with name '''wikidb'''
:3. Click on the ''wikidb'' in the list of databases to the left. You should see a set of tabs for this database appear in the right frame.
:4. Click on the '''Privileges''' tab and click on '''Add a new User'''
:5. Mention the following details
<pre>
User name: wikiuser
Host: localhost
Password: <type in a password>
Re-type: <re-type the above password>
</pre>
:6. Click on '''Check All''' in the '''Global Privileges''' section in the same page and then click '''Go'''

==== Download Mediawiki ====
Download mediawiki, extract to '''~/Sites''' and create a symbolic link
<pre>
$ wget http://noc.wikimedia.org/mediawiki-1.16.0.tar.gz

$ tar -xf mediawiki-1.16.0.tar.gz ~/Sites

$ cd ~/Sites

$ ln -s mediawiki-1.16.0 mediawiki
</pre>

==== Run Mediawiki installer ====
:The following steps are a concise form of the [http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Mac_OS_X#Web-based_setup detailed steps mentioned in the mediawiki installation guide for mac os x].

:1. Browse to http://localhost/~short-username/mediawiki. Fill in the details it asks for and wait while the installer does its work. Pay attention to the default values of database name and username. Change this to whatever you have defined.
:2. [http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Mac_OS_X#Web-based_setup Refer steps 7-13 to finish the rest of the setup].

Documentation

2012-01-25T20:31:44Z

Ppreddy@uab.edu: /* Developer Guide */ add MediawikiDev link below Cross Platform LAMP stack

Docs is a an open documentation platform for UAB built on the [[wikipedia:MediaWiki|Mediawiki]] engine, the same wiki engine that powers [[wikipedia:|Wikipedia]]. Content contributions to docs are welcome and encouraged. The breadth, depth, and value of our documentation is directly attributable to those who participate in its development.

Caveat Emptor: Some of information is of historical nature. We are actively reviewing and tagging outdated content to ensure it is updated.

= Editing Docs =

The only requirements to contribute content to Docs is to [http://apps.uabgrid.uab.edu/login authenticate using an identity of your choice] and respect the copyright of original material by following the [http://en.wikipedia.org/wiki/Wikipedia:List_of_guidelines#Content|contribution guidelines used by Wikipedia]. All material contributed to docs is governed by the [http://creativecommons.org/licenses/by-sa/3.0/us/ Creative Commons Attribution and Share-Alike license] referenced at the bottom of each page.

To create a new page, simply edit an existing page and add a reference to your new page by writing the new page's name inside double square brackets, as shown in the following example. Save your edit to the existing page along with a meaningful comment in the Summary text box noting the creation of a link to a new page. After saving this edit, you will see a link to your new page (in red). Follow that link to begin adding content to your new page.
<pre>
[[My new page]]
</pre>

Editing and refining content is as important as original contribution. The wiki model encourages capturing the natural evolution of knowledge. When editing content, please be sure to also make a note of the change in the Summary text box at the bottom of the edit window, eg. "spell check" for minor spelling corrections or "improve readability" for refining activities. If you intend to make major improvements or changes to content, please coordinate those changes with other editors of the content by engaging in a dialog on the pages' "Discussion" tab or by directly contacting the primary contributors for the page as identified on the "View History" tab. Again, the Wikipedia community practices provides value guidance on [[wikipedia:Wikipedia:List_of_guidelines#Editing|how to edit pages]].

Interwiki links provide convenient shortcuts to the content in other wikis. One of the most useful interwiki link is "wikipedia" which creates links to articles in Wikipedia itself. These interwiki links can provide valuable background for material you are covering in docs. For example, when document an application you can reference the Wikipedia page for associated content relevant to your domain. To create an interwiki link, use the double square bracket convention as you would to link to another local page and simply prefix the Wikipedia article name with "wikipedia:". For example, this link to the Wikipedia article on [[wikipedia:wiki|wiki]] is constructed as follows:
<pre>
[[wikipedia:Wiki|wiki]]
</pre>
The vertical bar separator is used to provide text that matches your page content rather than the raw content of the link name.

= FAQ =

* [[FAQ]]

= User Guide =

* Applications
** Collaboration
*** [[Git]]
*** [[Mediawiki]]
*** [[Sympa]]
*** [[Trac]]
*** [[Wordpress]]
** Scientific
*** [[BLAST]]
*** [[CNS]]
*** [[FreeSurfer]]
*** [[FSL]]
*** [[Galaxy]]
*** [[Impute]]
*** [[MatLab]]
*** [[MrBayes]]
*** [[SPPARKS]]
*** [[NAMD]]

* [[Trust_UABgrid_CA|Using UABgrid Web Sites]]

* [[Subversion]]

= Developer Guide =

The research computing system includes a collection of libraries designed to address a variety of needs. The libraries you use and how you interact with them, depends on which aspect of the system you want to leverage. It is possible to work exclusively with one library, using only it's default interface. More evolved tool users might leverage many different libraries and combine them in novel ways to create new applications or additional services. Nonetheless, even simple scripts that only tune a default feature are often the most appreciated.

Our goal is to get you started developing, a.k.a. creating, as quickly as possible. You will eventually want to become familiar with the system model so you can organize your work accordingly.

Generally speaking, as a developer, you will find yourself working in one of two areas of the system. You are either building scripts to support data analysis or virtual experiments using the compute library or you are working on web accessible libraries or applications. The compute library, a.k.a. the cluster Cheaha and all the tools it makes available, is very mature and is used autonomously by most developers today. Web accessible resources are at the leading edge of our research computing platform.

Developers building web accessible libraries and applications, typically, work closely with the core team since this part of the platform is under heavy construction and requires a higher level of coordination between team members.

The following guides provide a rough introduction to the environment.

* Developer Tools
** Web -- As with all web development, you need to have an environment where you can run a web application and interact with it via a web browser. For most applications, this requires some light weight web server that will run you code and expose an HTTP interface to your browser. Most web applications have some basic instructions for getting the application set up in a personal development environment. You can use these to get started.
*** Cross Platform LAMP stack [[XAMPP]]
**** [[MediawikiDev]]
*** OpenSUSE LAMP stack [http://en.opensuse.org/SDB:Linux_Apache_MySQL_PHP]. Note: if this is a private dev environment, don't bother opening up the firewall as described. You don't need it since a local web browser will be able to access everything by default.
*** [[API]]
** Command-line -- The command line environment accessible via SSH to Cheaha provides a full service Linux environment where you can build any code that you need. Familiar command line tools are available and more can be discovered with the `module avail` command.
* Identity Management
** [[IdentityPrimer]]
** [[UABgrid Web Applications|Identity for Web Apps]]
*** [[UABgrid_SP_Metadata]]
** [[Web Authentication]]
* Data Management
** [[Data Management Framework]]
* Application Frameworks
** HPC Workflow Tools
*** [[UABgrid Jobs|Understanding Workflows]]
*** [[Swift Notes|Swift]]
*** [[UsingGridWay|GridWay]]
** caGrid/DASI Tools
*** [[HowtoInstallCagrid]]: Installation notes for caGrid stack
*** [[HowtoDataModelling]]: Data/Object modelling using EA/caAdapter
*** [[HowtoBuildDataService]]: Data service build process using caCORE-SDK
*** [[HowtoBuildGridDataService]]: Grid service build process using Introduce
*** [[HowtoDeployWebService]]: Deployment steps for web service
*** [[HowtoDeployGridService]]: Deployment steps for grid service
*** [[HowtoQueryDataService]]: Quering data service using CQL/DCQL

= Administrator Guide =

* System Overview
** [[System Types]]

* Managing Permissions
** [[File Access Control]]

Git FAQ

2011-10-24T22:20:24Z

Ppreddy@uab.edu: start stub for Git_FAQ

__TOC__

=== How do you find if you delete a branch which was pushed? ===

=== How would you restore a deleted branch? ===

=== How to delete a file(s) entirely from git history? ===

=== How to select a few files to commit within a branch? ===

=== How to merge select files/commits from different branches? ===

GitRepoAccessOnUABgrid

2011-10-05T17:57:16Z

Ppreddy@uab.edu: add numbered lists

__TOC__
== Overview ==

UABgrid git repositories are hosted on git.uabgrid.uab.edu.

Access to git repos will be decided by the project you are currently part of (usually the project and repo namespace will be the same).

== Access Protocol ==

Currently ssh is the protocol available for accessing git repos on git.aubgrid. As a result, a user would need an account on the host git.aubgrid. This, eventually would be replaced by [https://github.com/sitaramc/gitolite Gitolite], which would preclude the need for creating actual unix accounts on git.uabgrid. Currently, when we create git user accounts, users will be given git-shell access which will permit them to run the following git commands:
# clone
# pull (fetch)
# archive

Push access is by default given to the ''maintainer'' of the project's source code. The ''maintainer'' is the authority to grant push privileges to members in a team.

Two steps to access a git repo
# Get a git account. Please send a request email to support@vo.aubgrid.uab.edu with subject ''git account on git.uabgrid'' and also specify the project that you are a member of.
# ssh public key. Email ssh public key from the machine(s) from where you will be doing your git work.

Upon an email confirmation that your account was created and your ssh pub keys added to the list of authorized_keys, you are ready to begin hacking on the code.

<pre>
git clone <blazer-id>@git.uabgrid.uab.edu:~git/repositories/<reponame>.git
</pre>

== References ==
* [http://man.he.net/man1/git-shell git-shell]

GitRepoAccessOnUABgrid

2011-10-05T17:55:38Z

Ppreddy@uab.edu: initial wiki stub for git repo access on uabgrid

__TOC__
== Overview ==

UABgrid git repositories are hosted on git.uabgrid.uab.edu.

Access to git repos will be decided by the project you are currently part of (usually the project and repo namespace will be the same).

== Access Protocol ==

Currently ssh is the protocol available for accessing git repos on git.aubgrid. As a result, a user would need an account on the host git.aubgrid. This, eventually would be replaced by [https://github.com/sitaramc/gitolite Gitolite], which would preclude the need for creating actual unix accounts on git.uabgrid. Currently, when we create git user accounts, users will be given git-shell access which will permit them to run the following git commands:
* clone
* pull (fetch)
* archive

Push access is by default given to the ''maintainer'' of the project's source code. The ''maintainer'' is the authority to grant push privileges to members in a team.

Two steps to access a git repo
1. Get a git account. Please send a request email to support@vo.aubgrid.uab.edu with subject ''git account on git.uabgrid'' and also specify the project that you are a member of.
2. ssh public key. Email ssh public key from the machine(s) from where you will be doing your git work.

Upon an email confirmation that your account was created and your ssh pub keys added to the list of authorized_keys, you are ready to begin hacking on the code.

<pre>
git clone <blazer-id>@git.uabgrid.uab.edu:~git/repositories/<reponame>.git
</pre>

== References ==
* [http://man.he.net/man1/git-shell git-shell]

FreeSurfer

2011-10-05T16:01:16Z

Ppreddy@uab.edu: /* Overview */ add latest version inof and release notes link to freesurfer

__TOC__
== Overview ==
[http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide FreeSurfer] is a freely available software package developed by investigators at the Athinoula A. Martinos Center for Biomedical Imaging used for a number of procedures including:

# Creation of computerized models of the brain from magnetic resonance imaging (MRI) data.
# Processing of functional magnetic resonance imaging (fMRI) data.
# Measuring a number of morphometric properties of the brain including cortical thickness and regional volumes.
# Intersubject averaging of structural and functional data using a procedure that aligns individuals based on their cortical folding patterns for optimal alignment of homologous neural regions.

The [http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes latest version of Freesurfer available is 5.1.0]. The last update to this software was 24 May 2011.

== FreeSurfer on Cheaha ==
FreeSurfer-4.5 version is installed on Cheaha. ''module'' command can be used to find out the current installed version. For Freesurfer, use
<pre>
module whatis freesurfer
</pre>

FreeSurfer run its process in a non-parallel environment, so there won't be much benefit from a dual/quad/hex core machine for a single case analysis. However a number of FreeSurfer recon-all processes can be started in the same machine, thereby, theoretically reducing the time to analyze a group of cases. Following is a tutorial to setup your Freesurfer environment and to run an example recon-all process on Cheaha.

=== SSH-key Config ===

Windows:
[http://docs.uabgrid.uab.edu/wiki/WorkingWithPutty#SSH_Keys Configure putty] to connect to Cheaha with ssh-keys.

Follow [http://docs.uabgrid.uab.edu/wiki/MatLab_SSH_Config#Linux this link] for ssh key config on linux.

Follow [http://docs.uabgrid.uab.edu/wiki/MatLab_SSH_Config#Mac this link] for ssh key config on mac.

=== Environment Setup ===

Setting up an environment to run FreeSurfer on Cheaha, consists of defining FreeSurfer related variables and their installation paths. Steps 1 and 2 are a one-time set up, ie., the first time you login to Cheaha. Need not set up and source env variables defined in .bashrc from the next time you login to Cheaha (as at login bashrc is auto-sourced).

1. To set up your environment on Cheaha, open $HOME/.bashrc with your favorite text editor such as vim, nano, emacs etc., and copy-paste the contents below:
<pre>
export FREESURFER_HOME=/share/apps/freesurfer/4.5
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export FSFAST_HOME=$FREESURFER_HOME/fsfast
export FSF_OUTPUT_FORMAT=nii
export MNI_DIR=$FREESURFER_HOME/mni
export FSL_DIR=$HOME/fsl
export PATH=$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$MNI_DIR/bin:$FSL_DIR/bin:$PATH
</pre>
NOTE: In the above bashrc, FSL_DIR is also defined. FSL is not part of FreeSurfer, but is installed and available to all users on Cheaha. To start using FSL/bedpostx [http://docs.uabgrid.uab.edu/wiki/FSL see this documentation.]

2. Source the above environment variables.
<pre>
source $HOME/.bashrc
</pre>

=== Example recon_all ===

1. Prepare by creating a subjects directory to hold image files in .nii format

<pre>
mkdir $HOME/subjects

cd $HOME/subjects
</pre>

2. Get example image by copying the line below

<pre>
wget http://repo.uabgrid.uab.edu/files/freesurfer/example.nii.gz

gunzip example.nii.gz
</pre>

==== Create job submission script ====

This is a simple SGE script to submit recon-all process. This script first copies your subjects directory from your $HOME containing the MRI data to Cheaha's high performance file system, $UABGRID_SCRATCH, so as to ramp the speed of recon-all process. The recon-all process is then executed on $UABGRID_SCRATCH.

NOTE: For the example run, we've created a subjects directory at $HOME to hold the example.nii image.
For your actual run with real images, if you've copied your images to another location, then make sure to change $HOME/subjects (line no 7) accordingly in the script below.

Open a text editor and copy-paste the below contents:
<pre>
#!/bin/bash

scratch=$UABGRID_SCRATCH
jobs=$scratch/jobs
sub=$scratch/subjects
mkdir $jobs
cp -r $HOME/subjects $scratch/

function run-recon-all() {
cd $scratch
#create submit script for each patient in the subjects directory
for patient in `ls -1 $sub`
do
unset SUBJECTS_DIR
SUBJECTS_DIR=$sub
export SUBJECTS_DIR
cat > $jobs/recon-all-$patient.sh <<EOF
#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#
#$ -N recon-all-$patient
# Set the hard and soft run time limits (ex: 1hour/58 min)
#$ -l h_rt=30:00:00,s_rt=29:55:00
#$ -j y
#$ -M YOUR_EMAIL_ADDRESS
#$ -m eas
# set up FreeSurfer environment variables

mri_convert -oi -os $SUBJECTS_DIR/$patient $SUBJECTS_DIR/$patient.mgz

sleep 15

recon-all -sd $SUBJECTS_DIR -s $patient
EOF
done

#submit job script for each patient in the jobs directory to the cluster
pushd $jobs
for script in `ls -1`
do
echo "submitting job $script"
qsub $script
done
popd
}
run-recon-all
</pre>

==== Make script executable ====

Make the above script executable
<pre>
chmod +x <name-of-script-above>
</pre>

==== Submit job script ====

Then submit that script with
<pre>
./name-of-script-above
</pre>

==== Track status of job ====

Check on the job status with qstat.
<pre>
qstat -u $USER
</pre>

==== Clean-up scratch ====

After the completion of the recon-all process, copy the results and logs back to your $HOME and delete the contents from scratch
<pre>
cp -r $UABGRID_SCRATCH/subjects $HOME/subjects-results

cp -r $UABGRID_SCRATCH/jobs $HOME/jobs-results

rm -rf $UABGRID_SCRATCH/subjects

rm -rf $UABGRID_SCRATCH/jobs
</pre>

== Transfer files from Cheaha to local computer ==

Transfer the subjects/jobs directory from your home account on Cheaha to your local computer with '''psftp'''. [http://docs.uabgrid.uab.edu/wiki/WorkingWithPutty#File_Transfer Here's how to transfer files using psftp].

== References ==

[http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer Freesurfer wiki]

[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data Freesurfer Tutorial]

[http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all recon-all]

[http://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert mri_convert]

FSL

2011-10-05T15:59:06Z

Ppreddy@uab.edu: add latest version info and download link for fsl

__TOC__
== Overview ==

[http://www.fmrib.ox.ac.uk/fsl/index.html FSL] is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK.

The [http://www.fmrib.ox.ac.uk/fsldownloads/ latest version of FSL available is 4.1.6]. The last update to this software was in 2008.

== FSL on Cheaha ==

[http://www.fmrib.ox.ac.uk/fsl/fsl/linux.html FSL-4.1.6] is installed on Cheaha. ''module'' command can be used to find out the current installed version. For FSL, use
<pre>
module whatis fsl
</pre>

== Environment Setup ==

Before running any FSL applications like ''bedpostx'', set up the necessary environment with the following command:
<pre>
module load fsl/fsl-4.1.6
</pre>

FSL

2011-10-04T20:03:43Z

Ppreddy@uab.edu: separate content into different headings

__TOC__
== Overview ==

[http://www.fmrib.ox.ac.uk/fsl/index.html FSL] is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK.

== FSL on Cheaha ==

[http://www.fmrib.ox.ac.uk/fsl/fsl/linux.html FSL-4.1.6] is installed on Cheaha. ''module'' command can be used to find out the current installed version. For FSL, use
<pre>
module whatis fsl
</pre>

== Environment Setup ==

Before running any FSL applications like ''bedpostx'', set up the necessary environment with the following command:
<pre>
module load fsl/fsl-4.1.6
</pre>

FreeSurfer

2011-10-04T19:59:11Z

Ppreddy@uab.edu: change heading names, add links to ssh config for linux and mac

__TOC__
== Overview ==
[http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide FreeSurfer] is a freely available software package developed by investigators at the Athinoula A. Martinos Center for Biomedical Imaging used for a number of procedures including:

# Creation of computerized models of the brain from magnetic resonance imaging (MRI) data.
# Processing of functional magnetic resonance imaging (fMRI) data.
# Measuring a number of morphometric properties of the brain including cortical thickness and regional volumes.
# Intersubject averaging of structural and functional data using a procedure that aligns individuals based on their cortical folding patterns for optimal alignment of homologous neural regions.

== FreeSurfer on Cheaha ==
FreeSurfer-4.5 version is installed on Cheaha. ''module'' command can be used to find out the current installed version. For Freesurfer, use
<pre>
module whatis freesurfer
</pre>

FreeSurfer run its process in a non-parallel environment, so there won't be much benefit from a dual/quad/hex core machine for a single case analysis. However a number of FreeSurfer recon-all processes can be started in the same machine, thereby, theoretically reducing the time to analyze a group of cases. Following is a tutorial to setup your Freesurfer environment and to run an example recon-all process on Cheaha.

=== SSH-key Config ===

Windows:
[http://docs.uabgrid.uab.edu/wiki/WorkingWithPutty#SSH_Keys Configure putty] to connect to Cheaha with ssh-keys.

Follow [http://docs.uabgrid.uab.edu/wiki/MatLab_SSH_Config#Linux this link] for ssh key config on linux.

Follow [http://docs.uabgrid.uab.edu/wiki/MatLab_SSH_Config#Mac this link] for ssh key config on mac.

=== Environment Setup ===

Setting up an environment to run FreeSurfer on Cheaha, consists of defining FreeSurfer related variables and their installation paths. Steps 1 and 2 are a one-time set up, ie., the first time you login to Cheaha. Need not set up and source env variables defined in .bashrc from the next time you login to Cheaha (as at login bashrc is auto-sourced).

1. To set up your environment on Cheaha, open $HOME/.bashrc with your favorite text editor such as vim, nano, emacs etc., and copy-paste the contents below:
<pre>
export FREESURFER_HOME=/share/apps/freesurfer/4.5
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export FSFAST_HOME=$FREESURFER_HOME/fsfast
export FSF_OUTPUT_FORMAT=nii
export MNI_DIR=$FREESURFER_HOME/mni
export FSL_DIR=$HOME/fsl
export PATH=$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$MNI_DIR/bin:$FSL_DIR/bin:$PATH
</pre>
NOTE: In the above bashrc, FSL_DIR is also defined. FSL is not part of FreeSurfer, but is installed and available to all users on Cheaha. To start using FSL/bedpostx [http://docs.uabgrid.uab.edu/wiki/FSL see this documentation.]

2. Source the above environment variables.
<pre>
source $HOME/.bashrc
</pre>

=== Example recon_all ===

1. Prepare by creating a subjects directory to hold image files in .nii format

<pre>
mkdir $HOME/subjects

cd $HOME/subjects
</pre>

2. Get example image by copying the line below

<pre>
wget http://repo.uabgrid.uab.edu/files/freesurfer/example.nii.gz

gunzip example.nii.gz
</pre>

==== Create job submission script ====

This is a simple SGE script to submit recon-all process. This script first copies your subjects directory from your $HOME containing the MRI data to Cheaha's high performance file system, $UABGRID_SCRATCH, so as to ramp the speed of recon-all process. The recon-all process is then executed on $UABGRID_SCRATCH.

NOTE: For the example run, we've created a subjects directory at $HOME to hold the example.nii image.
For your actual run with real images, if you've copied your images to another location, then make sure to change $HOME/subjects (line no 7) accordingly in the script below.

Open a text editor and copy-paste the below contents:
<pre>
#!/bin/bash

scratch=$UABGRID_SCRATCH
jobs=$scratch/jobs
sub=$scratch/subjects
mkdir $jobs
cp -r $HOME/subjects $scratch/

function run-recon-all() {
cd $scratch
#create submit script for each patient in the subjects directory
for patient in `ls -1 $sub`
do
unset SUBJECTS_DIR
SUBJECTS_DIR=$sub
export SUBJECTS_DIR
cat > $jobs/recon-all-$patient.sh <<EOF
#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#
#$ -N recon-all-$patient
# Set the hard and soft run time limits (ex: 1hour/58 min)
#$ -l h_rt=30:00:00,s_rt=29:55:00
#$ -j y
#$ -M YOUR_EMAIL_ADDRESS
#$ -m eas
# set up FreeSurfer environment variables

mri_convert -oi -os $SUBJECTS_DIR/$patient $SUBJECTS_DIR/$patient.mgz

sleep 15

recon-all -sd $SUBJECTS_DIR -s $patient
EOF
done

#submit job script for each patient in the jobs directory to the cluster
pushd $jobs
for script in `ls -1`
do
echo "submitting job $script"
qsub $script
done
popd
}
run-recon-all
</pre>

==== Make script executable ====

Make the above script executable
<pre>
chmod +x <name-of-script-above>
</pre>

==== Submit job script ====

Then submit that script with
<pre>
./name-of-script-above
</pre>

==== Track status of job ====

Check on the job status with qstat.
<pre>
qstat -u $USER
</pre>

==== Clean-up scratch ====

After the completion of the recon-all process, copy the results and logs back to your $HOME and delete the contents from scratch
<pre>
cp -r $UABGRID_SCRATCH/subjects $HOME/subjects-results

cp -r $UABGRID_SCRATCH/jobs $HOME/jobs-results

rm -rf $UABGRID_SCRATCH/subjects

rm -rf $UABGRID_SCRATCH/jobs
</pre>

== Transfer files from Cheaha to local computer ==

Transfer the subjects/jobs directory from your home account on Cheaha to your local computer with '''psftp'''. [http://docs.uabgrid.uab.edu/wiki/WorkingWithPutty#File_Transfer Here's how to transfer files using psftp].

== References ==

[http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer Freesurfer wiki]

[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data Freesurfer Tutorial]

[http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all recon-all]

[http://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert mri_convert]

File:Ha-20110816.odp

2011-09-29T17:38:10Z

Ppreddy@uab.edu: mysql high availability presentation in openoffice format. Test for uploading file of type odp

mysql high availability presentation in openoffice format. Test for uploading file of type odp

API

2011-09-13T02:29:33Z

Ppreddy@uab.edu: initial commit for api wiki

== Research Notebook ==

''[http://blogs.uabgrid.uab.edu/jpr/2011/09/a-public-record-sheer-curation-and-the-research-notebook/ The research computing platform] is an environment that records the context surrounding our [http://git-scm.com/ computations], [http://projects.uabgrid.uab.edu/r-group projects], [http://dev.uabgrid.uab.edu/ platform], [http://blogs.uabgrid.uab.edu/jpr ideas], and [http://docs.uabgrid.uab.edu/ knowledge]. Our goal is a public record of the state and evolution of the environment in which we conduct our research: documented processes that can be incorporated by research teams, influenced by research needs, and shared with peers. This environment is integral to the digital archive of our research effort. This is the research notebook.''

== RESTful Style Programming ==

At the core of the research computing platform is a collection of open source tools. Most of these tools have a web programmable interface that support a variety of functionality. The interfaces range from [http://en.wikipedia.org/wiki/SOAP SOAP] and [http://en.wikipedia.org/wiki/Xmlrpc XML-RPC] to [http://en.wikipedia.org/wiki/Restful RESTful]. The tool spaces which span the breadth of the research computing platform are:
* Resource management
:: web APIs for vm register/start/stop via OpenNebula

* Project management
:: web APIs to group management, mailing lists, Wordpress, Trac, MediaWiki and new code to tie them together

* Job Management
:: web APIs from Galaxy to control workflows

These fairly well align with the [http://en.wikipedia.org/wiki/Infrastructure_as_a_service#Layers Cloud paradigms] of Infrastructure (I), Platform (P), and Application (A) as a Service, ie. the IaaS, PaaS, and AaaS.

The goal of our research computing platform is to allow these to be extended into whatever areas interest people and which they are
willing to build out.

For example, developers can use these tools to build their own web services and expose them to the communities they want to support. Their users will need resource keys (akin to what you would use for Google or Facebook services, they could even run FB apps) if they are going to be resource intensive APIs or whatever. The sky is pretty much the limit here.

== How to ==

== API Overview ==

Here's a list of developer documentation on the available programmable interfaces for the core tools of the research computing platform
* OpenNebula Cloud API - offers two interfaces
: 1. [http://opennebula.org/documentation:rel3.0:occiug OGF OCCI API]
:: RESTful service based on the Open Grid Forum (OGF) Open Cloud Computing Interface (OCCI) API specification. OCCI is a Protocol and API for all kinds of management tasks, including deployment, autonomic scaling and monitoring.
: 2. [http://opennebula.org/documentation:rel3.0:ec2qug EC2 Query API]
:: a subset of the EC2 Query interface, enabling the creation of public clouds managed by OpenNebula

Documentation

2011-09-12T21:08:33Z

Ppreddy@uab.edu: /* Developer Guide */ add API section

The UABgrid Documentation provides an overview of content from specific interest perspectives.

It is a work in progress. As of 2009-11-11 it only includes pages already existing and provides guidance for how to structure collected information.

Caveat Emptor: Some of information is of historical nature, having been created early in the UABgrid Pilot (circa 2007Q3) before usage scenarios started shaping value.

= FAQ =

* [[FAQ]]

= User Guide =

* Applications
** Collaboration
*** [[Git]]
*** [[Mediawiki]]
*** [[Sympa]]
*** [[Trac]]
*** [[Wordpress]]
** Scientific
*** [[BLAST]]
*** [[CNS]]
*** [[FreeSurfer]]
*** [[FSL]]
*** [[Galaxy]]
*** [[Impute]]
*** [[MatLab]]
*** [[MrBayes]]
*** [[SPPARKS]]
*** [[NAMD]]

* [[Trust_UABgrid_CA|Using UABgrid Web Sites]]

* [[Subversion]]

= Developer Guide =

* Identity Management
** [[IdentityPrimer]]
** [[UABgrid Web Applications|Identity for Web Apps]]
*** [[UABgrid_SP_Metadata]]
* Application Frameworks
** HPC Workflow Tools
*** [[UABgrid Jobs|Understanding Workflows]]
*** [[Swift Notes|Swift]]
*** [[UsingGridWay|GridWay]]
** caGrid/DASI Tools
*** [[HowtoInstallCagrid]]: Installation notes for caGrid stack
*** [[HowtoDataModelling]]: Data/Object modelling using EA/caAdapter
*** [[HowtoBuildDataService]]: Data service build process using caCORE-SDK
*** [[HowtoBuildGridDataService]]: Grid service build process using Introduce
*** [[HowtoDeployWebService]]: Deployment steps for web service
*** [[HowtoDeployGridService]]: Deployment steps for grid service
*** [[HowtoQueryDataService]]: Quering data service using CQL/DCQL
** Developer Tools
*** [[XAMPP]]
*** [[API]]

= System Administrator Guide =

* System Overview
** [[System Types]]

UAB Research Computing Day 2011

2011-09-09T19:55:07Z

Ppreddy@uab.edu: /* Handout and Promotional Materials */ add rcday and hpc bootcamp flyer

The 2011 UAB Research Computing Day will be held '''September 15, 2011''' at the Hill University Center.

Activities this year will include a seminar on Thursday, September 15, 2011 with invited talks, campus researchers, and poster session. This will be followed on Friday September 16, 2011 by an HPC Bootcamp that includes a Next Generation Sequencing Workshop using Galaxy.

[[UAB Research Computing Day]] is dedicated to dialogs on science, engineering, and their ever present drive to advance the art of technology in opening new research frontiers. These dialogs connect with our daily operations, touch the far edges of the Internet, and intersect with the themes of national funding agencies and peer institutions. Please visit the [[UAB Research Computing Day|Research Computing Day]] page for an verview and history of past events.

== Event Days and Times ==

* 8:30 - 4pm, September 15, 2011, 2011 UAB Research Computing Day at the Hill University Center
* 9:00 - 3:30pm. September 16, 2011 [[2011_HPC_Boot_Camp|2011 HPC Boot Camp and Galaxy Workshop]] at the Hill University Center

== Registration ==

Please visit the [https://workspaces.ad.uab.edu/it/projects/projectspaces/2011_Research_Computing_Day_102/default.aspx registration page] to reserve your attendance today. Registration will ensure adequate resources are available for the even and is required to reserve a provided lunch.

A separate registration is required for the UAB HPC Bootcamp 2011, please [http://uabhpcbootcamp2011.eventbrite.com/ register here] and [[2011 HPC Boot Camp|view agenda here]]

== Agenda ==

{{:2011_Research_Computing_Day_Agenda}}

== Program Committee ==

{{:2011_Research_Computing_PC}}

== Handout and Promotional Materials ==

* [[Image:CI_agenda_15Sept2011.pdf‎|page agenda handout for event attendees]]
* [[Image:Rcday2011-flyer.pdf‎|page flyer for RCDay and HPC Bootcamp]]

[[Category:RCDay2011]]

File:Rcday2011-flyer.pdf

2011-09-09T19:52:08Z

Ppreddy@uab.edu: 2011 Research Computing Day (Sep 15) and HPC Bootcamp (Sep 16) flyer

2011 Research Computing Day (Sep 15) and HPC Bootcamp (Sep 16) flyer

File:HighAvailabilityOverview-MySQL-HA-Solutions-20110823.pdf

2011-08-24T15:08:34Z

Ppreddy@uab.edu: Overview of HA - components, solutions, and environments. Also has notes regarding each of the components of HA

Overview of HA - components, solutions, and environments. Also has notes regarding each of the components of HA

MacNotes

2011-07-26T23:33:33Z

Ppreddy@uab.edu: /* Useful Links */ add link to mac automator tool

[[Media:[[Media:Example.ogg]]]]== Mac OS user notes ==

=== Open Source Software ===
'''* [http://www.macports.org MacPorts]: Tool to access and install open-source software on the Mac OS X operating system.'''
# [http://svn.macports.org/repository/macports/downloads/MacPorts-1.7.1/MacPorts-1.7.1-10.5-Leopard.dmg Install MacPorts for Mac OS X 10.5 (Leopard)]
# [https://connect.apple.com/cgi-bin/WebObjects/MemberSite.woa/wa/getSoftware?bundleID=20414 Install Xcode] - integrated development environment for creating great Mac and iPhone applications. You would need an Apple Developer Connection (ADC) id, which can be created from the above link and then can download Xcode for free.
Refer [http://guide.macports.org/#installing here] for further details on installing MacPorts.

Similar to '''yum/apt-get''', '''port''' is the command used to interact with MacPorts. Common port commands are:
port list
port search <search-text>
port info <app-name>
port install <app-name>

More port commands can be found with

man 1 port

'''* [http://www.freesmug.org/ FreeSoftware Mac User Group]: Tutorials, info, and news about free and open source Mac software.'''

=== Software Install ===
* '''Microsoft Office 200'''8: Download ISO from [http://www.uab.edu/it/software/index.php UAB IT software library]. The Mac OS X is able to do installation directly from an ISO file.
==== Mozilla ====
* '''Firefox''': Download and install Firefox from the [http://www.mozilla.com/en-US/firefox/firefox.html Mozilla website]
* '''Thunderbird''': Download and Install Thunderbird from [http://www.mozillamessaging.com/en-US/thunderbird/ here].

===== Mailbox Alert Add-on to Thunderbird =====

By default, Thunderbird on Mac does not provide a pop up for new messages. To get pop-ups from thunderbird, every time you get a new message, [https://addons.mozilla.org/en-US/thunderbird/addon/2610 install this Mailbox Alert Add-on]. After installing the add-on,
# Select a folder in your account
# Go to Tools -> Mailbox Alert Preferences
# Check '''Show a message''' and type in a message in the second blank text field
# Check icon
# Check Play a sound
# Click Global Preferences and change Position, Effect, Pop up duration On click options to your liking.
Now you will get a pop up and the folder with the new message will be highlighted in blue with the number of new messages in parentheses beside the folder.

===== Notification system: Growl =====
I installed growl on my mac, which is a notification system for Mac. I found it quite useful for getting new email notification. It can be configured to give other system notifications as well. For more info.: http://growl.info/about.php

===== Daily notebook / journaling system: Journler =====
The 'journler' seems to be good application for taking and organizing notes. It also supports publishing to a blog and posting as an email. It has a keyboard shortcut for inserting date/time, which I find really useful in text editors. For more info.: http://journler.com/

===== Terminal application: iTerm =====
iTerm is an external terminal emulation program for Mac. It supports tabbed browsing and naming tabs is easy. We can bookmark our most frequently used sessions. I found it much better than native Mac's terminal program. For more info.: http://iterm.sourceforge.net/

===== MIME Edit Add-on to Thunderbird =====

To open file attachments of type *.doc, *.pdf etc., from Thunderbird, [https://addons.mozilla.org/en-US/thunderbird/addon/4498 install this MIME Edit Add-on]. After installing the Add-on,
# Go to menu Tools->MIME Edit...
# Go to Edit tab and click "New Type" button
# In "MIME type" and "Extension" textfields, type "PDF".
# Select the radiobutton "Open it with" and choose the path of acroread application by clicking the 'Choose' button.
# Click OK on all open dialogs and restart Thunderbird.

==== Image Editor ====

* GNU Image Manipulation Program (GIMP) is a powerful tool for the preparation and manipulation of digital images. The GIMP provides the user with a wide variety of image manipulation, painting, processing, and rendering tools.
* Homepage: http://www.gimp.org/
* Install Gimp on Mac OS 10.5 with MacPorts (make sure you [http://docs.uabgrid.uab.edu/wiki/MacNotes#Open_Source_Software install MacPorts first]) as follows:

sudo port install gimp2

NOTE: Takes quite a while to get started the first time the port install is run (~3-5m) and then some more to first download and install the dependencies like curl, perl etc. The list of gimp dependencies are:
$ port deps gimp2
gimp2 has build dependencies on:
pkgconfig
intltool
p5-xml-parser
gimp2 has library dependencies on:
iso-codes
gegl
gtk2
libmng
libexif
aalib
librsvg
poppler
gnome-vfs
libgnomeui
curl
libwmf
lcms
dbus-glib
py25-gtk

=== Configurations ===
* LDAP for address book: Check [http://main.uab.edu/Sites/it/faqs/49036 UAB IT FAQ page] for LDAP configuration settings.

=== MySQL ===

==== References ====
* [http://developer.apple.com/internet/opensource/osdb.html MySQL on Mac OS X]
* [http://www.malisphoto.com/tips/mysql-on-os-x.html Compling and Editing MSQL5 on Mac OS X 10.6]
* [http://dev.mysql.com/doc/refman/5.0/en/mac-os-x-installation.html MySQL ref Manual - Installing MySQL on Mac OS X]

=== Eclipse ===

Installing Eclipse on Mac is a no-brainer. Configuring is a bit tricky, especially, if you dont know your way around Mac.

To configure Eclipse with increased JVM heap size, so that you dont get '''OutOfMemoryError'''

# Edit '''eclipse.ini''' inside the Eclipse application bundle, to pass arguments to Eclipse
# select the Eclipse application bundle icon while holding down the Control Key. This will present you with a popup menu.
# select "Show Package Contents" in the popup menu. Locate eclipse.ini file in the Contents/MacOS subfolder and open it with your favorite text editor to edit the command line options.
# the options for increasing the JVM heap size are:
<pre>
-vmargs
-Xms128m
-Xmx512m
-XX:MaxPermSize=128m
</pre>

==== References ====
* [http://blog.xam.dk/?p=58 Max's blog Eclipse and Memory Settings]
* [http://publib.boulder.ibm.com/infocenter/wasinfo/v6r1/index.jsp?topic=/org.eclipse.platform.doc.user/tasks/running_eclipse.htm IBM's Running Eclipse]

=== Java -1.5 ===

Mac OS X 10.5 (leopard) and 10.6 (snow leopard) are installed with only Java-1.6. For applications requiring Java-1.5 (like caGrid apps - catissue etc), download Apple's version of Java-1.5

* [http://support.apple.com/downloads/Java_for_Mac_OS_X_10_5_Update_7 Java for Mac OS X 10.5 update 7]

==== References ====

[http://chxor.chxo.com/post/183013153/installing-java-1-5-on-snow-leopard Installing Java-1.5 on snow leopard]

=== JBoss 4.2.2.GA ===

Starting the Jboss container on Mac OS X (10.6) results in the following error
<pre>
./bin/run.sh: line 89: ulimit: open files: cannot modify limit: Invalid argument
</pre>

JBoss forum has [https://jira.jboss.org/jira/browse/JBAS-4948 a thread] on the above error. Provided in the thread is patch ( not the attachment) in the last email (dated 03-29-2010). This patch sets the variable ''MAX_FD_LIMIT'' in case of a ''darwin'' based system with ''sysctl'' command instead of ''ulimit''. The complete and a more current patch is as follows:
<pre>
--- run.sh.orig 2010-04-16 12:50:20.000000000 -0500
+++ run.sh 2010-04-16 12:51:32.000000000 -0500
@@ -78,8 +78,11 @@
export JBOSS_HOME

# Increase the maximum file descriptors if we can
-if [ "$cygwin" = "false" ]; then
+if [ "$darwin" = "false" ]; then
MAX_FD_LIMIT=`ulimit -H -n`
+else
+ MAX_FD_LIMIT=`sysctl -n kern.maxfilesperproc`
+fi
if [ $? -eq 0 ]; then
if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ]; then
# use the system max
@@ -93,7 +96,6 @@
else
warn "Could not query system maximum file descriptor limit: $MAX_FD_LIMIT"
fi
-fi

# Setup the JVM
if [ "x$JAVA" = "x" ]; then
</pre>

Save the above as ''patch.txt'' and apply the patch to Jboss startup script (run.sh) as follows:
<pre>
cd $JBOSS_HOME/bin

patch -b run.sh < patch.txt
</pre>

=== Create ''pidof'' command ===
''pidof'' utility does not exist in Mac OS X. Create one as follows:
<pre>
#!/bin/sh
ps axc|awk "{if (\$5==\"$1\") print \$1}";
</pre>

Save the above in '''/bin/pidof'''. Change permissions

<pre>
chmod 755 /bin/pidof
</pre>

To list the process id, run the command with a service/app name, for eg.,

<pre>
pidof iTunes
</pre>

Reference: http://www.macosxhints.com/article.php?story=20030618114543169

=== Useful Links ===
* [http://support.apple.com/kb/HT1343 Mac OS X keyboard shortcuts]
* A very useful tool is the '''Automator''' in mac - http://support.apple.com/kb/ht2488

=== Tips for getting Mac-friendly or otherwise ===
* '''Disable auto unzipping of Safari downloaded zip file''': Safari automatically unzips downloaded zip file. You can disable it by Safari-Preferences -> General tab -> Uncheck 'Open safe files after downloading' . Also note that Safari/Mac does not show any window/prompt/status when the download starts.
* '''Changing Terminal window title''': echo -n -e "\033]0; <your-title> \007"
* '''Home/End keys''': When editing text, Home/End keys on Mac keyboard function differently than on Windows, i.e., when trying to traverse from one end of a sentence to the other. You should instead use the following:
** To get to the end of the sentence, use Command+Left Arrow
** To get to the beginning of the sentence, use Command+Right Arrow
* '''Print screen''':
** Whole screen - Command+Shift+3
** Select screen area - Command+Shift+4
** Also can make use of the [http://eduscapes.com/tap/topic7.htm#1 Mac Grab Utility]

Template:Cluster Application

2011-06-09T21:45:26Z

Ppreddy@uab.edu: add named parameters to versions section

This is a template to create Cluster Application page
Introduction

==Using Application on the Cluster==
===Application versions ===
Name: {{{name}}}
Version: {{{version}}}

===Submitting jobs to the cluster ===

==Application Support ==
===Application User groups===
===Application Wiki ===
===Application User Group archives===

==Application Tutorials and Learning Resources==

[[Category: ABCXYZ]]

SubversionOverHttps

2011-04-19T20:55:09Z

Ppreddy@uab.edu: /* Edit SVN servers file */ add IE specific global setting to svn/servers file

Following instructions document how to configure subversion client to use HTTPS/SSL for accessing UABgrid repository. The setup has been tested on Linux CentOS 5.4 and Tortoise SVN with Windows XP. The setup may not work with Max OS-X 10.6.

== Download certificates ==
=== Download user certificate ===
* Log in to [https://ca.uabgrid.uab.edu/user/ UABgrid Certificate Authority ]
* Request UABgrid certificate from Certificate Management Menu. After completing certificate request you will be prompted to download the certificate, but ignore this prompt as you will need the certificate in different format to use with SVN client.
* Now go back to Certificate Management Menu and click on download link for 'Cert+Key PKCS12' file format. The download link will prompt you for a passphrase to protect your private key. For security reasons, you should use a a strong passphrase to protect private key in this file. Please remember this passphrase as you will need to enter it for interacting with SVN repository.
* Save this PKCS12 file in a safe location (home directory) on your system. This certificate is referred as usercert.pfx in rest of this documentation.

=== Download UABgrid CA certificate ===
* Visit [http://uabgrid.uab.edu/UABgridCA UABgrid CA] page to download UABgrid root CA certificate. Right-click on 'FireFox, Konqueror, and similar browsers (PEM format)' link and select 'Save as..' option to save certificate on your system. This certificate is referred as cacert.pem. Firefox may save this file as 'cacert.pem.xhtml', so you may need to use filename as cacert.pem.xhtml. IE saves this certificate as 'cacert.cer'.

== Configure SVN client to use certificates ==
=== Edit SVN servers file ===
* Now you will need to configure Subversion client to use certificates for repository access. This configuration is added in servers file.
* On Windows XP with Tortoise SVN this file is
<pre>
C:\Documents and Settings\<Username>\Application Data\Subversion\servers
</pre>
and on Linux this file is
<pre>
~/.subversion/servers
</pre>
We will add a group for uabgrid repositories with usercert.pfx to establish user identity and also add cacert.pem to trust UABgrid CA.
* Add usercert.pfx entry:
<pre>
### In the 'groups' section, the URL of the repository you're
### trying to access is matched against the patterns on the right.
### If a match is found, the server options are taken from the
### section with the corresponding name on the left.

[groups]
uabgrid = *.uabgrid.uab.edu
# othergroup = repository.blarggitywhoomph.com
# thirdgroup = *.example.com

[uabgrid]
ssl-client-cert-file = /path/to/certificate/usercert.pfx

</pre>
* Add cacert.pem entry to 'global' section. This is typically last section in the file:
<pre>
[global]
ssl-authority-files = /path/to/certificate/cacert.pem
</pre>
For certificate downloaded in IE, add cacert.cer entry to 'global' section. This is typically last section in the file:
<pre>
[global]
ssl-authority-files = /path/to/certificate/cacert.cer
</pre>

* Additionally you may have following configuration parameters available depending on your Subversion client. This includes whether you want to store your passphrase. You may want disable storing your passphrase. Here is a link to [http://svnbook.red-bean.com/nightly/en/svn.serverconfig.httpd.html#svn.serverconfig.httpd.authn.sslcerts SSL certificate management topic in SVN book].
<pre>
# Password / passphrase caching parameters:
# store-passwords = no
# store-plaintext-passwords = no
# store-ssl-client-cert-pp = no
# store-ssl-client-cert-pp-plaintext = no
</pre>

=== Test your setup ===
* Test your setup by listing remote repository contents.
<pre>
svn list https://repository-url>
</pre>

SubversionOverHttps

2011-04-19T20:52:09Z

Ppreddy@uab.edu: /* Download UABgrid CA certificate */ add IE's mechanism of saving cacert i.,e with file extension - .cer

Following instructions document how to configure subversion client to use HTTPS/SSL for accessing UABgrid repository. The setup has been tested on Linux CentOS 5.4 and Tortoise SVN with Windows XP. The setup may not work with Max OS-X 10.6.

== Download certificates ==
=== Download user certificate ===
* Log in to [https://ca.uabgrid.uab.edu/user/ UABgrid Certificate Authority ]
* Request UABgrid certificate from Certificate Management Menu. After completing certificate request you will be prompted to download the certificate, but ignore this prompt as you will need the certificate in different format to use with SVN client.
* Now go back to Certificate Management Menu and click on download link for 'Cert+Key PKCS12' file format. The download link will prompt you for a passphrase to protect your private key. For security reasons, you should use a a strong passphrase to protect private key in this file. Please remember this passphrase as you will need to enter it for interacting with SVN repository.
* Save this PKCS12 file in a safe location (home directory) on your system. This certificate is referred as usercert.pfx in rest of this documentation.

=== Download UABgrid CA certificate ===
* Visit [http://uabgrid.uab.edu/UABgridCA UABgrid CA] page to download UABgrid root CA certificate. Right-click on 'FireFox, Konqueror, and similar browsers (PEM format)' link and select 'Save as..' option to save certificate on your system. This certificate is referred as cacert.pem. Firefox may save this file as 'cacert.pem.xhtml', so you may need to use filename as cacert.pem.xhtml. IE saves this certificate as 'cacert.cer'.

== Configure SVN client to use certificates ==
=== Edit SVN servers file ===
* Now you will need to configure Subversion client to use certificates for repository access. This configuration is added in servers file.
* On Windows XP with Tortoise SVN this file is
<pre>
C:\Documents and Settings\<Username>\Application Data\Subversion\servers
</pre>
and on Linux this file is
<pre>
~/.subversion/servers
</pre>
We will add a group for uabgrid repositories with usercert.pfx to establish user identity and also add cacert.pem to trust UABgrid CA.
* Add usercert.pfx entry:
<pre>
### In the 'groups' section, the URL of the repository you're
### trying to access is matched against the patterns on the right.
### If a match is found, the server options are taken from the
### section with the corresponding name on the left.

[groups]
uabgrid = *.uabgrid.uab.edu
# othergroup = repository.blarggitywhoomph.com
# thirdgroup = *.example.com

[uabgrid]
ssl-client-cert-file = /path/to/certificate/usercert.pfx

</pre>
* Add cacert.pem entry to 'global' section. This is typically last section in the file:
<pre>
[global]
ssl-authority-files = /path/to/certificate/cacert.pem
</pre>

* Additionally you may have following configuration parameters available depending on your Subversion client. This includes whether you want to store your passphrase. You may want disable storing your passphrase. Here is a link to [http://svnbook.red-bean.com/nightly/en/svn.serverconfig.httpd.html#svn.serverconfig.httpd.authn.sslcerts SSL certificate management topic in SVN book].
<pre>
# Password / passphrase caching parameters:
# store-passwords = no
# store-plaintext-passwords = no
# store-ssl-client-cert-pp = no
# store-ssl-client-cert-pp-plaintext = no
</pre>

=== Test your setup ===
* Test your setup by listing remote repository contents.
<pre>
svn list https://repository-url>
</pre>

DeployingGalaxyToAmazonEC2

2010-12-14T17:55:24Z

Ppreddy@uab.edu: initial wiki page for user exp on GC to EC2

__TOC__

== Overview ==

User experience on deploying the [http://bitbucket.org/galaxy/galaxy-central/wiki/cloud Galaxy Cloud] to the Amazon EC2.

== Amazon Web Services Account Setup ==

Wordpress

2010-12-14T17:38:53Z

Ppreddy@uab.edu: delete extra ref section

__TOC__

== Overview ==
[http://wordpress.org/about/ WordPress] is a open source blog publishing application, but has evolved into a content management system through plugins and widgets. WordPress is built on PHP, MySQL and licensed under GPL.

== End Users ==
For end users interested in using Mediawiki for document collaboration send an email to...

Coming soon, a self servicing web interface for provisioning a mediawiki instance (TBD, a landing page...)

== Developers ==
For developers interested in customizing WordPress (themes, plugins etc), an AMP (Apache, MySQL, PHP) stack facilitates a quick setup. Recommended here, is one easy way to set up an AMP stack which has cross-platform capability ie., [http://docs.uabgrid.uab.edu/wiki/XAMPP XAMPP] developed by Apache Friends.

=== Mac OS X ===
==== XAMPP ====
:1. [http://docs.uabgrid.uab.edu/wiki/XAMPP Install and configure XAMPP for Mac]. Here we are installing XAMPP-beta.
:'''NOTE''': Wordpress requires atleast PHP version of 4.3 and MySQL of 4.2 and XAMPP-beta provides the latest versions, MySQL (5.1.46) and PHP (5.3.2), which is compatible with the latest Wordpress software.
:2. Start up xampp as root, either from xampp's control or from command line. This starts both Apache and mysql services.
<pre>
$ sudo /Applications/XAMPP/xamppfiles/xampp start
</pre>

==== Database ====

:1. Set up a database for wordpres using xampp's '''phpmyadmin''' console. Go to http://localhost/phpmyadmin/ to open up phpmyadmin console
:2. Create a database with name '''wordpress'''
:NOTE: you can leave the database defaults for username and password, which for xampp's mysql is '''root''' and no password.
:If you have [http://docs.uabgrid.uab.edu/wiki/XAMPP#Mac_OS_X_3 secured xampp], make sure you change privileges for the user '''root''' for ''wordpress'' db accordingly.

==== Download WordPress ====
The following steps are from the [http://codex.wordpress.org/Installing_WordPress#Famous_5-Minute_Install wordpress famous 5-minute install].

Download wordpress, extract to '''~/Sites'''
<pre>
$ wget http://wordpress.org/latest.zip

$ unzip wordpress-3.0.3.zip -d ~/Sites

</pre>

==== Run WordPress Installer ====
:1. Browse to http://localhost/~short-username/wordpress
:2. Wordpress offers to [http://codex.wordpress.org/Installing_WordPress#Setup_configuration_file create and edit the '''wp-config.php''']. Fill in the database details as mentioned in the phpmyadmin console for '''wordpress''' database.
:3. [http://codex.wordpress.org/Installing_WordPress#Finishing_installation Finish installation]

== References ==
: [http://codex.wordpress.org/Installing_WordPress#Common_Installation_Problems Wordpress installation troubleshoot]
: [http://codex.wordpress.org/New_To_WordPress_-_Where_to_Start Wordpress getting started guide]

Wordpress

2010-12-14T17:38:14Z

Ppreddy@uab.edu: /* Download WordPress */ delete change dir from preformatted text

Wordpress

2010-12-14T17:37:34Z

Ppreddy@uab.edu: /* Developers */ add wp install steps

__TOC__

== Overview ==
[http://wordpress.org/about/ WordPress] is a open source blog publishing application, but has evolved into a content management system through plugins and widgets. WordPress is built on PHP, MySQL and licensed under GPL.

== End Users ==
For end users interested in using Mediawiki for document collaboration send an email to...

Coming soon, a self servicing web interface for provisioning a mediawiki instance (TBD, a landing page...)

== Developers ==
For developers interested in customizing WordPress (themes, plugins etc), an AMP (Apache, MySQL, PHP) stack facilitates a quick setup. Recommended here, is one easy way to set up an AMP stack which has cross-platform capability ie., [http://docs.uabgrid.uab.edu/wiki/XAMPP XAMPP] developed by Apache Friends.

=== Mac OS X ===
==== XAMPP ====
:1. [http://docs.uabgrid.uab.edu/wiki/XAMPP Install and configure XAMPP for Mac]. Here we are installing XAMPP-beta.
:'''NOTE''': Wordpress requires atleast PHP version of 4.3 and MySQL of 4.2 and XAMPP-beta provides the latest versions, MySQL (5.1.46) and PHP (5.3.2), which is compatible with the latest Wordpress software.
:2. Start up xampp as root, either from xampp's control or from command line. This starts both Apache and mysql services.
<pre>
$ sudo /Applications/XAMPP/xamppfiles/xampp start
</pre>

==== Database ====

:1. Set up a database for wordpres using xampp's '''phpmyadmin''' console. Go to http://localhost/phpmyadmin/ to open up phpmyadmin console
:2. Create a database with name '''wordpress'''
:NOTE: you can leave the database defaults for username and password, which for xampp's mysql is '''root''' and no password.
:If you have [http://docs.uabgrid.uab.edu/wiki/XAMPP#Mac_OS_X_3 secured xampp], make sure you change privileges for the user '''root''' for ''wordpress'' db accordingly.

==== Download WordPress ====
The following steps are from the [http://codex.wordpress.org/Installing_WordPress#Famous_5-Minute_Install wordpress famous 5-minute install].

Download wordpress, extract to '''~/Sites'''
<pre>
$ wget http://wordpress.org/latest.zip

$ unzip wordpress-3.0.3.zip -d ~/Sites

$ cd ~/Sites

</pre>
==== Run WordPress Installer ====
:1. Browse to http://localhost/~short-username/wordpress
:2. Wordpress offers to [http://codex.wordpress.org/Installing_WordPress#Setup_configuration_file create and edit the '''wp-config.php''']. Fill in the database details as mentioned in the phpmyadmin console for '''wordpress''' database.
:3. [http://codex.wordpress.org/Installing_WordPress#Finishing_installation Finish installation]

== References ==
: [http://codex.wordpress.org/Installing_WordPress#Common_Installation_Problems Wordpress installation troubleshoot]
: [http://codex.wordpress.org/New_To_WordPress_-_Where_to_Start Wordpress getting started guide]

== References ==

Wordpress

2010-12-14T16:50:48Z

Ppreddy@uab.edu: /* End Users */ add end user info

Wordpress

2010-12-14T16:49:55Z

Ppreddy@uab.edu: /* Overview */ add wp intro

Mediawiki

2010-12-14T16:37:08Z

Ppreddy@uab.edu: /* References */ indent refs

__TOC__

== Overview ==

[http://www.mediawiki.org/wiki/MediaWiki Mediawiki] is a wiki software to enable communities to write documents collaboratively [http://en.wikipedia.org/wiki/Wiki#Characteristics]. Mediawiki, written in PHP, is what powers [http://www.wikipedia.org/ Wikipedia] and also [http://docs.uabgrid.uab.edu/wiki/Welcome UABgrid documentation]. The markup for Mediawiki is similar to other open-source wiki software like Trac, ie., it has WYSIWIG editing capabilities to translate formatting instructions to corresponding HTML tags.

== End Users ==

For end users interested in using Mediawiki for document collaboration send an email to...

Coming soon, a self servicing web interface for provisioning a mediawiki instance (TBD, a landing page...)

== Developers ==

For developers interested in customizing Mediawiki (themes, plugins etc), an AMP (Apache, MySQL, PHP) stack is required. Recommended here, is one easy way to set up an AMP stack which has cross-platform capability ie., [http://docs.uabgrid.uab.edu/wiki/XAMPP XAMPP] developed by Apache Friends.

=== Mac OS X ===
==== XAMPP ====
:1. [http://docs.uabgrid.uab.edu/wiki/XAMPP Install and configure XAMPP for Mac].
:'''NOTE''': Mediawiki requires atleast PHP version of 5.3.2 or later. PHP - 5.3.1 version is incompatible with Mediawiki and this is the version which comes with the current stable releases of XAMPP.
:::So, for Mediawiki development, [http://www.apachefriends.org/en/xampp-beta.html '''use XAMPP beta'''].
:2. Start up xampp as root, either from xampp's control or from command line. This starts both Apache and mysql services.
<pre>
$ sudo /Applications/XAMPP/xamppfiles/xampp start
</pre>

==== Database ====

:1. Set up a database for mediawiki using xampp's '''phpmyadmin''' console. Go to http://localhost/phpmyadmin/ to open up phpmyadmin console
:2. Create a database with name '''wikidb'''
:3. Click on the ''wikidb'' in the list of databases to the left. You should see a set of tabs for this database appear in the right frame.
:4. Click on the '''Privileges''' tab and click on '''Add a new User'''
:5. Mention the following details
<pre>
User name: wikiuser
Host: localhost
Password: <type in a password>
Re-type: <re-type the above password>
</pre>
:6. Click on '''Check All''' in the '''Global Privileges''' section in the same page and then click '''Go'''

==== Download Mediawiki ====
Download mediawiki, extract to '''~/Sites''' and create a symbolic link
<pre>
$ wget http://noc.wikimedia.org/mediawiki-1.16.0.tar.gz

$ tar -xf mediawiki-1.16.0.tar.gz ~/Sites

$ cd ~/Sites

$ ln -s mediawiki-1.16.0 mediawiki
</pre>

==== Run Mediawiki installer ====
:The following steps are a concise form of the [http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Mac_OS_X#Web-based_setup detailed steps mentioned in the mediawiki installation guide for mac os x].

:1. Browse to http://localhost/~short-username/mediawiki. Fill in the details it asks for and wait while the installer does its work. Pay attention to the default values of database name and username. Change this to whatever you have defined.
:2. [http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Mac_OS_X#Web-based_setup Refer steps 7-13 to finish the rest of the setup].

== References ==

: [http://www.mediawiki.org/wiki/MediaWiki Mediawiki]
: [http://download.wikimedia.org/mediawiki/1.16/mediawiki-1.16.0.tar.gz Download Mediawiki]
: [http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Mac_OS_X#Setting_up_MediaWiki Setting up Mediawiki]

Mediawiki

2010-12-14T16:36:00Z

Ppreddy@uab.edu: /* References */

__TOC__

== Overview ==

[http://www.mediawiki.org/wiki/MediaWiki Mediawiki] is a wiki software to enable communities to write documents collaboratively [http://en.wikipedia.org/wiki/Wiki#Characteristics]. Mediawiki, written in PHP, is what powers [http://www.wikipedia.org/ Wikipedia] and also [http://docs.uabgrid.uab.edu/wiki/Welcome UABgrid documentation]. The markup for Mediawiki is similar to other open-source wiki software like Trac, ie., it has WYSIWIG editing capabilities to translate formatting instructions to corresponding HTML tags.

== End Users ==

For end users interested in using Mediawiki for document collaboration send an email to...

Coming soon, a self servicing web interface for provisioning a mediawiki instance (TBD, a landing page...)

== Developers ==

For developers interested in customizing Mediawiki (themes, plugins etc), an AMP (Apache, MySQL, PHP) stack is required. Recommended here, is one easy way to set up an AMP stack which has cross-platform capability ie., [http://docs.uabgrid.uab.edu/wiki/XAMPP XAMPP] developed by Apache Friends.

=== Mac OS X ===
==== XAMPP ====
:1. [http://docs.uabgrid.uab.edu/wiki/XAMPP Install and configure XAMPP for Mac].
:'''NOTE''': Mediawiki requires atleast PHP version of 5.3.2 or later. PHP - 5.3.1 version is incompatible with Mediawiki and this is the version which comes with the current stable releases of XAMPP.
:::So, for Mediawiki development, [http://www.apachefriends.org/en/xampp-beta.html '''use XAMPP beta'''].
:2. Start up xampp as root, either from xampp's control or from command line. This starts both Apache and mysql services.
<pre>
$ sudo /Applications/XAMPP/xamppfiles/xampp start
</pre>

==== Database ====

:1. Set up a database for mediawiki using xampp's '''phpmyadmin''' console. Go to http://localhost/phpmyadmin/ to open up phpmyadmin console
:2. Create a database with name '''wikidb'''
:3. Click on the ''wikidb'' in the list of databases to the left. You should see a set of tabs for this database appear in the right frame.
:4. Click on the '''Privileges''' tab and click on '''Add a new User'''
:5. Mention the following details
<pre>
User name: wikiuser
Host: localhost
Password: <type in a password>
Re-type: <re-type the above password>
</pre>
:6. Click on '''Check All''' in the '''Global Privileges''' section in the same page and then click '''Go'''

==== Download Mediawiki ====
Download mediawiki, extract to '''~/Sites''' and create a symbolic link
<pre>
$ wget http://noc.wikimedia.org/mediawiki-1.16.0.tar.gz

$ tar -xf mediawiki-1.16.0.tar.gz ~/Sites

$ cd ~/Sites

$ ln -s mediawiki-1.16.0 mediawiki
</pre>

==== Run Mediawiki installer ====
:The following steps are a concise form of the [http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Mac_OS_X#Web-based_setup detailed steps mentioned in the mediawiki installation guide for mac os x].

:1. Browse to http://localhost/~short-username/mediawiki. Fill in the details it asks for and wait while the installer does its work. Pay attention to the default values of database name and username. Change this to whatever you have defined.
:2. [http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Mac_OS_X#Web-based_setup Refer steps 7-13 to finish the rest of the setup].

== References ==

# [http://www.mediawiki.org/wiki/MediaWiki Mediawiki]
# [http://download.wikimedia.org/mediawiki/1.16/mediawiki-1.16.0.tar.gz Download Mediawiki]
# [http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Mac_OS_X#Setting_up_MediaWiki Setting up Mediawiki]

Mediawiki

2010-12-14T16:32:42Z

Ppreddy@uab.edu: /* Run Mediawiki installer */ add mediawiki installer finish steps

__TOC__

== Overview ==

[http://www.mediawiki.org/wiki/MediaWiki Mediawiki] is a wiki software to enable communities to write documents collaboratively [http://en.wikipedia.org/wiki/Wiki#Characteristics]. Mediawiki, written in PHP, is what powers [http://www.wikipedia.org/ Wikipedia] and also [http://docs.uabgrid.uab.edu/wiki/Welcome UABgrid documentation]. The markup for Mediawiki is similar to other open-source wiki software like Trac, ie., it has WYSIWIG editing capabilities to translate formatting instructions to corresponding HTML tags.

== End Users ==

For end users interested in using Mediawiki for document collaboration send an email to...

Coming soon, a self servicing web interface for provisioning a mediawiki instance (TBD, a landing page...)

== Developers ==

For developers interested in customizing Mediawiki (themes, plugins etc), an AMP (Apache, MySQL, PHP) stack is required. Recommended here, is one easy way to set up an AMP stack which has cross-platform capability ie., [http://docs.uabgrid.uab.edu/wiki/XAMPP XAMPP] developed by Apache Friends.

=== Mac OS X ===
==== XAMPP ====
:1. [http://docs.uabgrid.uab.edu/wiki/XAMPP Install and configure XAMPP for Mac].
:'''NOTE''': Mediawiki requires atleast PHP version of 5.3.2 or later. PHP - 5.3.1 version is incompatible with Mediawiki and this is the version which comes with the current stable releases of XAMPP.
:::So, for Mediawiki development, [http://www.apachefriends.org/en/xampp-beta.html '''use XAMPP beta'''].
:2. Start up xampp as root, either from xampp's control or from command line. This starts both Apache and mysql services.
<pre>
$ sudo /Applications/XAMPP/xamppfiles/xampp start
</pre>

==== Database ====

:1. Set up a database for mediawiki using xampp's '''phpmyadmin''' console. Go to http://localhost/phpmyadmin/ to open up phpmyadmin console
:2. Create a database with name '''wikidb'''
:3. Click on the ''wikidb'' in the list of databases to the left. You should see a set of tabs for this database appear in the right frame.
:4. Click on the '''Privileges''' tab and click on '''Add a new User'''
:5. Mention the following details
<pre>
User name: wikiuser
Host: localhost
Password: <type in a password>
Re-type: <re-type the above password>
</pre>
:6. Click on '''Check All''' in the '''Global Privileges''' section in the same page and then click '''Go'''

==== Download Mediawiki ====
Download mediawiki, extract to '''~/Sites''' and create a symbolic link
<pre>
$ wget http://noc.wikimedia.org/mediawiki-1.16.0.tar.gz

$ tar -xf mediawiki-1.16.0.tar.gz ~/Sites

$ cd ~/Sites

$ ln -s mediawiki-1.16.0 mediawiki
</pre>

==== Run Mediawiki installer ====
:The following steps are a concise form of the [http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Mac_OS_X#Web-based_setup detailed steps mentioned in the mediawiki installation guide for mac os x].

:1. Browse to http://localhost/~short-username/mediawiki. Fill in the details it asks for and wait while the installer does its work. Pay attention to the default values of database name and username. Change this to whatever you have defined.
:2. [http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Mac_OS_X#Web-based_setup Refer steps 7-13 to finish the rest of the setup].

== References ==

Mediawiki

2010-12-10T22:12:51Z

Ppreddy@uab.edu: start on mediawiki installer steps

__TOC__

== Overview ==

[http://www.mediawiki.org/wiki/MediaWiki Mediawiki] is a wiki software to enable communities to write documents collaboratively [http://en.wikipedia.org/wiki/Wiki#Characteristics]. Mediawiki, written in PHP, is what powers [http://www.wikipedia.org/ Wikipedia] and also [http://docs.uabgrid.uab.edu/wiki/Welcome UABgrid documentation]. The markup for Mediawiki is similar to other open-source wiki software like Trac, ie., it has WYSIWIG editing capabilities to translate formatting instructions to corresponding HTML tags.

== End Users ==

For end users interested in using Mediawiki for document collaboration send an email to...

Coming soon, a self servicing web interface for provisioning a mediawiki instance (TBD, a landing page...)

== Developers ==

For developers interested in customizing Mediawiki (themes, plugins etc), an AMP (Apache, MySQL, PHP) stack is required. Recommended here, is one easy way to set up an AMP stack which has cross-platform capability ie., [http://docs.uabgrid.uab.edu/wiki/XAMPP XAMPP] developed by Apache Friends.

=== Mac OS X ===
==== XAMPP ====
:1. [http://docs.uabgrid.uab.edu/wiki/XAMPP Install and configure XAMPP for Mac].
:'''NOTE''': Mediawiki requires atleast PHP version of 5.3.2 or later. PHP - 5.3.1 version is incompatible with Mediawiki and this is the version which comes with the current stable releases of XAMPP.
:::So, for Mediawiki development, [http://www.apachefriends.org/en/xampp-beta.html '''use XAMPP beta'''].
:2. Start up xampp as root, either from xampp's control or from command line. This starts both Apache and mysql services.
<pre>
$ sudo /Applications/XAMPP/xamppfiles/xampp start
</pre>

==== Database ====

:1. Set up a database for mediawiki using xampp's '''phpmyadmin''' console. Go to http://localhost/phpmyadmin/ to open up phpmyadmin console
:2. Create a database with name '''wikidb'''
:3. Click on the ''wikidb'' in the list of databases to the left. You should see a set of tabs for this database appear in the right frame.
:4. Click on the '''Privileges''' tab and click on '''Add a new User'''
:5. Mention the following details
<pre>
User name: wikiuser
Host: localhost
Password: <type in a password>
Re-type: <re-type the above password>
</pre>
:6. Click on '''Check All''' in the '''Global Privileges''' section in the same page and then click '''Go'''

==== Download Mediawiki ====
Download mediawiki, extract to '''~/Sites''' and create a symbolic link
<pre>
$ wget http://noc.wikimedia.org/mediawiki-1.16.0.tar.gz

$ tar -xf mediawiki-1.16.0.tar.gz ~/Sites

$ cd ~/Sites

$ ln -s mediawiki-1.16.0 mediawiki
</pre>

==== Run Mediawiki installer ====
:The following steps are a concise form of the [http://www.mediawiki.org/wiki/Manual:Running_MediaWiki_on_Mac_OS_X#Web-based_setup detailed steps mentioned in the mediawiki installation guide for mac os x].

:1. Browse to http://localhost/~short-username/mediawiki.

== References ==

Mediawiki

2010-12-10T18:52:53Z

Ppreddy@uab.edu: fill in initial details- text and sections

__TOC__

== Overview ==

[http://www.mediawiki.org/wiki/MediaWiki Mediawiki] is a wiki software to enable communities to write documents collaboratively [http://en.wikipedia.org/wiki/Wiki#Characteristics]. Mediawiki, written in PHP, is what powers [http://www.wikipedia.org/ Wikipedia] and also [http://docs.uabgrid.uab.edu/wiki/Welcome UABgrid documentation]. The markup for Mediawiki is similar to other open-source wiki software like Trac, ie., it has WYSIWIG editing capabilities to translate formatting instructions to corresponding HTML tags.

== End Users ==

For end users interested in using Mediawiki for document collaboration send an email to...

Coming soon, a self servicing web interface for provisioning a mediawiki instance (TBD, a landing page...)

== Developers ==

For developers interested in customizing Mediawiki (themes, plugins etc), an AMP (Apache, MySQL, PHP) stack is required. Recommended here, is one easy way to set up an AMP stack which has cross-platform capability ie., [http://docs.uabgrid.uab.edu/wiki/XAMPP XAMPP] developed by Apache Friends.

=== Mac OS X ===
==== Setup XAMPP ====
:1. [http://docs.uabgrid.uab.edu/wiki/XAMPP Install and configure XAMPP for Mac].
:'''NOTE''': Mediawiki requires atleast PHP version of 5.3.2 or later. PHP - 5.3.1 version is incompatible with Mediawiki and this is the version which comes with the current stable releases of XAMPP.
:::So, for Mediawiki development, [http://www.apachefriends.org/en/xampp-beta.html '''use XAMPP beta'''].
:2. Start up xampp as root, either from xampp's control or from command line. This starts both Apache and mysql services.
<pre>
$ sudo /Applications/XAMPP/xamppfiles/xampp start
</pre>

==== Setup Database ====

:1. Set up a database for mediawiki using xampp's '''phpmyadmin''' console. Go to http://localhost/phpmyadmin/ to open up phpmyadmin console
:2. Create a database with name '''wikidb'''
:3. Click on the ''wikidb'' in the list of databases to the left. You should see a set of tabs for this database appear in the right frame.
:4. Click on the '''Privileges''' tab and click on '''Add a new User'''
:5. Mention the following details
<pre>
User name: wikiuser
Host: localhost
Password: <type in a password>
Re-type: <re-type the above password>
</pre>
:6. Click on '''Check All''' in the '''Global Privileges''' section in the same page and then click '''Go''

==== Download Mediawiki ====
Download mediawiki, extract to '''~/Sites''' and create a symbolic link
<pre>
$ wget http://noc.wikimedia.org/mediawiki-1.16.0.tar.gz

$ tar -xf mediawiki-1.16.0.tar.gz ~/Sites

$ cd ~/Sites

$ ln -s mediawiki-1.16.0 mediawiki
</pre>

==== Run Mediawiki installer ====

== References ==

Mediawiki

2010-12-08T20:53:20Z

Ppreddy@uab.edu: stub wiki for mediawiki

__TOC__

== Overview ==

== End Users ==

== Developers ==

== References ==

Wordpress

2010-12-08T20:52:31Z

Ppreddy@uab.edu: stub wiki forwordpress

__TOC__

== Overview ==

== End Users ==

== Developers ==

== References ==