Difference between revisions of "MEGA"

Revision as of 19:08, 29 June 2016

Description

From the MEGA web site: MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.

Version

4.02

Authorized Users

CIRCE account holders
RRA account holders
SC account holders

Platforms

CIRCE cluster
RRA cluster
SC cluster

Modules

MEGA requires the following module file to run:

apps/mega/4.02

See Modules for more information.

Running MEGA on CIRCE

Installing MEGA

Prior to the first time running MEGA, you will need to install the application to your work directory. This is necessary because the application attempts to writes configuration settings to the application directory. Because of this behavior the program works much better when it is copied to a users work directory.

[johndoe@login1 ~]$ mkdir /work/j/johndoe/mega
[johndoe@login1 ~]$ cd /work/j/johndoe/mega
[johndoe@login1 mega]$ /opt/apps/mega/4.02/install-mega

Starting MEGA

Establishing a GUI connection to CIRCE/SC

To use MEGA, you will need to connect to CIRCE/SC with GUI redirection, either using:

CIRCE/SC Desktop Environment
SSH with X11 redirection
- If connecting from OSX or Linux via SSH, please ensure that you use one of the following commands to properly redirect X11:
  - ```
  [user@localhost ~]$ ssh -X circe.rc.usf.edu
```
  or
- ```
[user@localhost ~]$ ssh -X sc.rc.usf.edu
```

Once connected to CIRCE, you can open MEGA using the steps below:

[user@login0 ~]$ module add apps/mega/4.02
[user@login0 ~]$ mega

Documentation

Home Page, User Guides, and Manuals

MEGA Home Page
- http://www.megasoftware.net/

Reporting Bugs

Report bugs with MEGA to the IT Help Desk: rc-help@usf.edu

@@ Line 3: / Line 3: @@
 ''From the MEGA web site'': MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.
-* [http://www.megasoftware.net/ MEGA Home Page]
+{{AppStandardHeader|4.02|mega}}
-== Version ==
-*4.02
-== Authorized Users ==
-*<code>CIRCE</code> account holders
-== Platforms ==
-*<code>CIRCE</code> cluster
 == Running MEGA on CIRCE ==
-The following describes what is necessary to run MEGA on CIRCE.
-=== [[Modules]] ===
-MEGA requires the following module file and some prerequisites to run:
-*<code>apps/mega/4.02</code>
 === Installing MEGA ===
@@ Line 35: / Line 16: @@
 [johndoe@login1 ~]$ cd /work/j/johndoe/mega
 [johndoe@login1 mega]$ /opt/apps/mega/4.02/install-mega</pre>
 === Starting MEGA ===
-Before you login to <code>CIRCE</code>, you need to make sure you have X11 Forwarding enabled. If you’re logging in from a UNIX/Linux system, you will need to do the following:
+{{X11Connection}}
-<pre style="white-space:pre-wrap; width:25%; border:1px solid lightgrey; background:#000000; color:white;">
-ssh -Y user@circe.rc.usf.edu</pre>
-&nbsp;<br>
-Simply type <code> mega </code> at the command prompt AFTER loading the proper module (see above) in your terminal window. If you have properly configured an X11 session, you should see the full MEGA interface. If this is your first time using MEGA, you will need to follow the on screen instructions for the Mozilla ActiveX plugin and then MEGA should load normally.
-For Windows, Mac, and Linux users, MEGA can also be launched through the CIRCE Desktop Environment using a terminal. For more information about the CIRCE Desktop Environment, please see our [[CIRCE Desktop|CIRCE Desktop Environment]] documentation.
+Once connected to CIRCE, you can open MEGA using the steps below:
-=== Additional Documentation ===
+<pre style="white-space:pre-wrap; width:40%; border:1px solid lightgrey; background:#000000; color:white;">[user@login0 ~]$ module add apps/mega/4.02
+[user@login0 ~]$ mega</pre>
+{{Documentation}}
 * MEGA Home Page
 ** http://www.megasoftware.net/
 {{ReportingBugs}}