Help with ABACAS

kyoru · 03-22-2012, 09:10 PM

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

akjones · 07-12-2013, 01:25 PM

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

03-22-2012, 09:10 PM	#1
kyoru Junior Member Location: puncak alam Join Date: Jan 2012 Posts: 2	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

07-12-2013, 01:25 PM	#2
akjones Member Location: North America Join Date: Jun 2013 Posts: 24	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