BioPerl

Hearing no objections, I've merged topic/move_WrapperBase with master. I will proceed to remove WrapperBase and friends from bioperl-live. MAJ On 2014-08-23 15:29, Mark A. Jensen wrote: _______________________________________________ Bioperl-l ... [More] mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l [Less]

All, Can people have a look at bioperl/bioperl-run branch topic/move_WrapperBase (https://github.com/bioperl/bioperl-run/tree/topic/move_WrapperBase) and see what they think. I used filter-branch to generate a (local clone of) bioperl-live ... [More] containing only Bio/Tools/Run and t/tools, then merged this into a topic/move_WrapperBase branch of bioperl-run. If this looks ok, give me the signal and I will merge into master. Next step would be to remove these items from bioperl-live. thanks MAJ On 2014-08-22 12:59, Fields, Christopher J wrote: _______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l [Less]

No updates to 1.6.x if they have been moved out (with the exception of Bio::Root). We need to end-of-life 1.6.x at some point. It's worth having a meeting to talk about what needs to be done and to maybe discuss 1.7.x(Google or IRC). IRC may be ... [More] easier.I can set up a poll, maybe see who wants to participate... WrapperBase is essentially the common core for all the wrappers (a few don’t use it, but most do). So it really belongs in bioperl-run, as well as StandAloneBlast. The only real reason this and the other Tool::Run modules were in bioperl-live was legacy, but I think this hampers bioperl-run development frankly, as it relies on bioperl-live (via WrapperBase). If all the wrapper code were part of bioperl-run fixes would be much easier to make and release independently. Yes, go ahead and do that. -c > [Less]

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I have also looked I don't mind the moving of those modules but I would like to ask something. Any future updates to the moved modules should also be added, if possible, to the modules that will remain v1.6.x branch? Or their development would be ... [More] freezed?? Or should they also be removed from there too?? I've been keeping the synchronicity of updated modules that were moved out of -live into their own repo with their versions in v1.6.x branch (like Root and Coordinate), but the synch of WrapperBase when mixed into other existing repo like Run will depend on if it start to depend on code of other Run modules or not. On a side note, I just realized that there is an empty "hmmer3.pm" file in "bioperl-live/Bio/Tools/Run"... It seems to have been added already empty in https://github.com/bioperl/bioperl-live/commit/64ab09ecd40abb8cd06e9b80aafcda323d1dc47e, maybe by mistake. It appears to be the only empty file in the repo. Should I delete it?? Cheers, Francisco J. Ossandon -----Mensaje original----- De: bio [Less]

Actually, it might be better to have all the BLAST-related stuff as one distribution, unless we can get bioperl-run installing much more cleanly (little overhead with few dependencies). Is that what you want to do? If so: cool! You should have ... [More] commit to bioperl-run BTW, you are listed as part of the developer team. chris On Aug 22, 2014, at 7:09 AM, Mark A. Jensen <maj< at >fortinbras.us> wrote: > [Less]

Thanks Chris-- yes, you must be right. I just did a quick grep for "StandAloneBlast" in the modules. I will verify and leave bl2seq alone. Will do everything in branches and then give the signal- cheers MAJ On 2014-08-21 23:50, Fields, Christopher J ... [More] wrote: _______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l [Less]

Agreed. Also, I think you mean that StandAloneBlast has a dependency on AlignIO::bl2seq, not the other way around, correct? At least, I didn’t see anything there. If no one objects to it (give it a day), I say go ahead and move it over. chris

> [...] > My simple proposal is to move these three modules from bioperl-live to > bioperl-run. (Only AlignIO/bl2seq.pm depends on StandAloneBlast, btw). > > Thoughts? > [...] Speaking from a safe distance, that sounds *wonderful*. g.

All, I'm starting to look at cleaning up bioperl-run so that, e.g., tests don't bork without a reasonable error message, are skipped appropriately, etc. As I do this, I'm finding that to fix certain issues, I need to consider mods to ... [More] Bio::Tools::Run::WrapperBase and friends. Alas, these are in the bioperl-live distro! Now, grepping for 'WrapperBase' in bioperl-live modules reveals only two that mention it: Bio/Tools/Run/WrapperBase/CommandExts.pm Bio/Tools/Run/StandAloneBlast.pm Bio/Tools/Run/WrapperBase.pm My simple proposal is to move these three modules from bioperl-live to bioperl-run. (Only AlignIO/bl2seq.pm depends on StandAloneBlast, btw). Thoughts? MAJ [Less]