[Bioperl-l] bioperl-run 1.5.1 RC1 up
jason.stajich at duke.edu
Sun Sep 25 16:38:05 EDT 2005
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% ??
can someone at least look at the Phrap and Primer3 stuff.
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.
> 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.
> Jason Stajich
> Duke University
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
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