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Windows port of contig assembly program

James Bonfield jkb at arran.mrc-lmb.cam.ac.uk
Thu Aug 31 05:47:26 EST 2000

In <kRc*zF4Ao at news.chiark.greenend.org.uk> Tim Cutts <timc at chiark.greenend.org.uk> writes:

> 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.

Source code is freely available, but you have to sign a source code licence to
obtain it. (The reason it used to be free was simply that you used to have to
sign a licence, but when we made it freely downloadable we removed the
source.) It's obviously also the case that commercial users need to have paid
for a copy of the package before we give them the source code (for free).

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

Indeed. It's being distributed by eBioinformatics at present (maybe more
later, but they're the only ones now).

HOWEVER, please note that the windows one is not free. The politics of this
are long winded so I won't bother to go into it, but it's sufficient to say
that charging for it on Windows will actually secure our long-term aim of
keeping the package free on Unix (including Linux).

Personally I think that having the Staden Package totally free in the GNU
sense would really help it. (However it may also mean that we don't get any
more grants! Any advice or suggestions?) Of course my personal opinions don't
matter a great deal as MRC is the copyright holder.

> 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

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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