SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics

Reply
 
Thread Tools
Old 03-22-2012, 09:10 PM   #1
kyoru
Junior Member
 
Location: puncak alam

Join Date: Jan 2012
Posts: 2
Default Help with ABACAS

I'm currently trying to use ABACAS: Algorithm-based automatic contiguation of assembled sequences. However, I'm a bit confused as how to get it running.

So far, I've tested it on windows, and it runs just fine. The problem is when it needs to run MUMmer. I've gone through ABACAS manuals, but none of them seem to go into detail regarding MUMmer. But it has been mentioned that ABACAS itself can be run on Windows.

Turning to MUMmer's manuals, i've discovered that MUMmer doesn't run on Windows. So, I'm a bit confused regarding whether or not it is possible to use ABACAS on Windows (Since ABACAS uses MUMmer).

Is there a way to go about this? :s

Last edited by kyoru; 03-22-2012 at 09:11 PM. Reason: grammatical error
kyoru is offline   Reply With Quote
Old 07-12-2013, 01:25 PM   #2
akjones
Member
 
Location: North America

Join Date: Jun 2013
Posts: 24
Default

Hello,

I realize this is an old post and you have probably long since either solved the problem or given up, but you can download and run ABACAS/ the entire PAGIT suite on a virtual machine using virtual box (https://www.virtualbox.org/). Download the virtual box suitable for your Windows system and then download either the 32bit or 64bit virtual machine compilation and follow the installation instructions on the webpage (http://www.sanger.ac.uk/resources/software/pagit/). ABACAS/MUMmer should work fine in this environment. I've been able to run MUMmer using a virtual machine on a MacOSX.

~akjones
akjones is offline   Reply With Quote
Reply

Tags
abacas, bioinformatics, linux, mummer, windows

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:02 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO