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Old 06-07-2010, 06:40 AM   #1
Adamo
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Default BFAST - Install

Hello,

I'm almost a beginner in bioinformatic, that's why my question may be (must be?) stupid...
I've downloaded bfast and my computer is running on windows. I've been trying to use the commands I've been told by the INSTALL.txt but it's been a complete failure for now!

I can't get any further information in the manual.

Could someone tell me how can I install bfast, and describe the procedure?

Thanks,


Adamo
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Old 06-07-2010, 06:56 AM   #2
Adamo
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It seems like I need Linux to use it but when I downloaded it there was a small icon of Windows (and solaris, bsd,...) next to the download link. That's why I assume it can work on my computer...?
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Old 06-07-2010, 08:07 AM   #3
maubp
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Having had a quick look at the file, you need a Unix like system. Linux should be fine. I think Mac OS X could probably work (I had a problem with "make check" saying it couldn't fine md5sum, I've not looked into it).

If you really have to use Windows, and the BFAST authors don't have a better idea, you could try using Cygwin - http://www.cygwin.com - but this isn't always so straightforward.
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Old 06-07-2010, 09:26 AM   #4
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Quote:
Originally Posted by maubp View Post
Having had a quick look at the file, you need a Unix like system. Linux should be fine. I think Mac OS X could probably work (I had a problem with "make check" saying it couldn't fine md5sum, I've not looked into it).

If you really have to use Windows, and the BFAST authors don't have a better idea, you could try using Cygwin - http://www.cygwin.com - but this isn't always so straightforward.
BFAST was designed for a Unix operating system, but may work with Cygwin installed. Do you have a compute cluster or is this a local project. It would probably be best to get accustomed to a HPC environment with respect to next-gen sequencing as soon as possible (my 2 cents).
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Old 06-08-2010, 12:02 AM   #5
Adamo
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Quote:
Originally Posted by maubp View Post
Having had a quick look at the file, you need a Unix like system. Linux should be fine. I think Mac OS X could probably work (I had a problem with "make check" saying it couldn't fine md5sum, I've not looked into it).

If you really have to use Windows, and the BFAST authors don't have a better idea, you could try using Cygwin - http://www.cygwin.com - but this isn't always so straightforward.
I have tried to use Cygwin, but I couldn't manage to get the script executed...
I'm a bit non linux-friendly...! I'll try some tutorial.
And I'll also try to run it on Linux asap.

If you know the command I should write into Cygwin, let me please know.
I've tried Cygwin using "$ path/script.sh" but the program seems not to recognize some commands...
Otherwise I'll wait for the bioinformatic guy in charge of it to come back at the lab!
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