Comments (8)
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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Related Issues (20)
- only a star in a sequence
- Installation issue HOT 1
- tinf->rbs_wt hadn't been reset before used HOT 1
- [Documentations/Examples] Could a few examples be added to the main readme or a linked site?
- Genes are predicted across N stretches even when providing the -m flag HOT 3
- real difference between meta and single when the -p
- Asterix at the end of translated protein sequences
- fasta files - empty lines handling
- Virus prediction
- -w command for summary statistic returns error HOT 3
- Predicted CDSs of plasmid AF149757.1 have interior stop codons
- Does training prodigal on multiple genomes instead of just one increase accuracy? HOT 1
- Gene calling on very short viral sequences
- Differences in gene prediction for forward and reverse sequences
- Prodigal v2.6.3 no stop_type output HOT 1
- gcc: error: language CORE-AVX2 not recognized HOT 1
- What Details of '-g' parameters are? HOT 1
- Please make a release HOT 2
- The minimum and maximum length of predicted genes
- Issue with output file content HOT 1
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