Windows port of contig assembly program

Tim Cutts timc at chiark.greenend.org.uk
Thu Aug 31 04:03:34 EST 2000


In article <002401c0131e$f2aacb80$7b02a8c0 at nic.in>,
Malay <curiouser at ccmb.ap.nic.in> wrote:
>Thanks Don And Neil:
>
>What I really want to do is this:
>
>I want scriptable access to the programs. I am not sure about Seqpup ( I am
>helpless Don :-( ). I am using a 32 MB RAM Intel machine where Swing Classes
>simply refuses to run. A DOS executable/ will be exactly what I want. And
>the program should be absolutely free (GNU sense), so that I can play around
>with the code.

The Staden package is one of the few that are well scriptable (by virtue
of its having a user interface implemented in Tcl/Tk).  It's free
(money-wise) to academics, but it is not free in the GNU sense.

You don't get full source code any more (shame) although you do of
course have freedom to tinker with the Tcl/Tk aspects of the program.

Staden does run on Windows NT (and probably 95 as well)

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.

I think it all depends on how much effort you're willing to put into
development yourself.  If you are, then joining in the FAKtory effort
could be worth your while.  See:

 http://bcf.arl.arizona.edu/faktory/

That site is not up yet, but it provides an e-mail address you can
contact.

Tim.








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