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Was->Re: Windows port of contig assembly program

niravm at my-deja.com niravm at my-deja.com
Wed Sep 6 14:16:20 EST 2000




Sorry for wandering from the Subject:

FAktory is OpenSource and currently [Linux|Solaris|OSF|IRIX] binaries
and basic tutorial, documentation can be downloaded from:
ftp://bcf.arl.arizona.edu/pub/faktory/
source, CVS access , wiki website will be available after 1st Oct 2000.
at:
http://bcf.arl.arizona.edu/faktory

FAKtory is developed using C, Tcl/Tk 8.0 using ET [Embedded Tk] package.
Porting the UI to MS windows may not be bad, but the FAKII kernel will
be a task. We don't have resources to do that.

There is no scripting components and not flexible like Staden, but each
"stage" of the assembly "pipeline" is highly configurable i.e. you can
define your own pipeline with as many vector, tag screening stages as
you like.

We may be looking at a new Kernel that can handle repeats and moving the
UI to Tcl/Tk 8.3 in the near future.

Feel free to email me at: [nirav at arl.arizona.edu_nospam ] if you have
questions or need src before Oct 1 !

The powerpoint presentation for FAKtory from BOSC 2000 can be found at:
ftp://bcf.arl.arizona.edu/pub/faktory/BOSC_2000.ppt
and has screen shots etc.

regards,
Nirav



> > You might also want to look at FAKtory, which is a similar idea to
> > Staden, and is Open Source.  It's not as advanced, but its GUI is
again
> > Tcl/Tk, so it should (a) be reasonably portable to Windows and (b)
be
> > scriptable, if it's been put together sensibly.  However, at the
talk at
> > BOSC 2000 about it, it seemed to me that although they had used
Tcl/Tk,
> > they hadn't thought about it in terms of a scripting interface to
the
> > software.
>
> FAKtory uses the FAKII assembly program, which does a pretty good job
-
> certainly better than our native assembler, which is why we have an
interface
> to it in the Staden Package. I haven't seen the GUI components of
FAKtory
> though.
>
> James
> --
> James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax:
01223 213556
> Medical Research Council - Laboratory of Molecular Biology,
> Hills Road, Cambridge, CB2 2QH, England.
> Also see Staden Package WWW site at
http://www.mrc-lmb.cam.ac.uk/pubseq/



>
> FAKtory uses the FAKII assembly program, which does a pretty good job
-
> certainly better than our native assembler, which is why we have an
interface
> to it in the Staden Package. I haven't seen the GUI components of
FAKtory
> though.
>
> James
> --
> James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax:
01223 213556
> Medical Research Council - Laboratory of Molecular Biology,
> Hills Road, Cambridge, CB2 2QH, England.
> Also see Staden Package WWW site at
http://www.mrc-lmb.cam.ac.uk/pubseq/
>


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