[Bioperl-l] bioperl-run 1.5.1 RC1 up

[Jason Stajich]

okay - I made some fixes,
go ahead and try RC2 instead.

There are problems with the EMBOSS and PHYLIP wrappers because of  
course the parameters have changed.  I don't have time to track this  
down, we talked about adding switches  to handle different version  
and have a different parsing menu, but I don't have the time or  
energy to do it.  This seems like a pretty big showstopper for  
bioperl-run, I hope some other folks can help out.

t/Consense.t    9  2304     7    0   0.00%  ??
t/DrawGram.t    2   512     4    0   0.00%  ??
t/DrawTree.t    2   512     4    0   0.00%  ??
t/EMBOSS.t      2   512    30    1   3.33%  7
t/Neighbor.t    2   512    14    0   0.00%  ??
t/Phrap.t                   5    2  40.00%  4-5
t/Primer3.t                 7    1  14.29%  7
t/ProtDist.t               11    1   9.09%  9
t/ProtPars.t    2   512     7    0   0.00%  ??
t/SeqBoot.t     2   512     6    0   0.00%  ??


http://bioperl.org/DIST/bioperl-run-1.5.1-rc2.tar.gz
http://bioperl.org/DIST/bioperl-run-1.5.1-rc2.zip

can someone at least look at the Phrap and Primer3 stuff.

Thanks,
-jason
On Sep 24, 2005, at 1:07 PM, Jason Stajich wrote:

> The bioperl-run RC1 package is up as well thanks to fixes from  
> several people.  I think that this package will still need some  
> more testing and fixes before it will be ready for release, but I  
> encourage folks to take it out for a spin.
>
> http://bioperl.org/DIST/bioperl-run-1.5.1-rc1.tar.gz
> http://bioperl.org/DIST/bioperl-run-1.5.1-rc1.zip
>
> There was at least one bug reported with tmhmm and the --noplot  
> option - I had the code to fix it, but have not checked it in  
> because I do not have copy of tmhmm on my system to test it  
> against.  We'll need someone with that in house to do the fixing  
> and re-test.   I can provide the patch file to the in-progress fix  
> if someone wants to take that on.
>
>
> Thanks,
> -jason
>
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
>
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12