Make a new release? about prodigal HOT 8 CLOSED

Some bugs have been fixed

Do you mean the pending pull request? I don't see any updates to the main repo.

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@smdabdoub there has been many changes since the 2.6.1 release on Aug 21, 2014 on the GoogleImport branch which I think is still the default for 2.x

https://github.com/hyattpd/Prodigal/commits/GoogleImport

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The only commit in the default branch that's not included in the release of 2.6.3 is #34 Undefined behavior leads to different program outputs when compiled with GCC 4-6 vs GCC 7

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I can reproduce #34 with gcc 8.2.0-2 (Currently in Debian testing). So, that problem will be more widespread in the long run (when this enters Ubuntu and so on). Because #34 makes the output have an invalid GFF3 format, it also broke a pipeline I ran (CrisprCasFinder).

Installed with linux brew.

EDIT:

Since some might find this helpfull and, also since coincedentally a linuxbrew maintainer and writer of the Prodigal formula is in this thread (hi @sjackman ). Here is how to install the latest and fixed version of prodigal using linuxbrew.

First, create a head reference in the brew formula: Edit this formula with brew edit prodigal, and add the following line after the class definition (and maybe this formula will also be updated accordingly by @sjackman ).

class Prodigal < Formula                                                        
  head "https://github.com/hyattpd/Prodigal.git", :branch => "GoogleImport" 
  ...

You can now install from this created head with

brew install --HEAD prodigal 

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Another option is to add…

revision 1
…
patch do
  url "https://patch-diff.githubusercontent.com/raw/hyattpd/Prodigal/pull/35.patch?full_index=1"
  sha256 "fd292c0a98412a7f2ed06d86e0e3f96a9ad698f6772990321ad56985323b99a6"
end

@hwalinga I'd be happy to merge a PR to Brewsci/bio to add that patch.

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Why does #34 produce an invalid GFF3? That shouldn't happen (did it change the output in some way?)

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Renato (@unode) reports that issue #34 was fixed by PR #35.

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At this point, not really planning any new releases of C version unless there arises a serious bug that causes segmentation faults or the like.

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