Shantanu was kind enough to share some feedback on installing BFAST.  I have added a section in the manual in the latest git code.  Please take a look and provide feedback based on your own experience(s).

On another note, do we feel comfortable for another release to incorporate some of the more recent changes?


Nils Homer

---------- Forwarded message ----------
From: Shantanu K. Karve <>
Date: Tue, Feb 22, 2011 at 4:43 PM
Subject: Feedback on BFAST installation


I thought my notes, as I install Bfast on UBUNTU 10.4 may help you when developing the next version..Naturally everything that works won't get mentioned - so this will sound like just complaints - just being brief and to  the point.

1. I note there is a bfast-server at sourceForge - sounds like what I'd be interested in - I'm looking at a multicore multi PC setup.. But I note the date and leave it at that.

2.  I note the combo bfast and bwa and wonder about it but let it for now.

3. The Readme said "For manual pages, including installation directions, please see:
manual/bfast-book.pdf" But they AREN"T in it !
4. Find the Installation instructions file.. Hm no binaries ? Ok.. start it .


Fails.. googling it gives me that I need to load  automake.install that

seems ok ( though there was something about git not found )

fails, install zlib1g-dev
fails, install libbz2-dev

fails again on gzread etc.. but they are there ! googling suggests that that -lz parameter on gcc is in the wrong place, but hey that was a automake thing !

ok rerun from the beginning so the files are remade.. do so.
seems ok.

make  check fails
No rule to make target `', needed by `check-TESTS'.  Stop.

No such file in the tests directory anyway so comment out that test
make check keeps failing.. eventually since I've messed with and perhaps something else.. give up with the tests.

install works fine.

Then try the examples. It tells me to get the phi file from off the net but that location doesn't work anymore. BUT... the phi*.fa files are there in /test/data folder. Run the example from the manual .. It works fine - from the computing and Installation Verification Procedure viewpoint.

Thanks for sharing your work.

I come to this from a math angle not biology.