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nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
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IQtree executable name for IQtree 2.x is iqtree2 #379

Closed tillea closed 11 months ago

tillea commented 1 year ago

Hi, when packaging gubbins 3.3.0 for Debian and running its test suite I realised that gubbins can't find the iqtree executable. While I tried to rename this inside the gubbins code in a patch there might be some other instances of a reference to /usr/bin/iqtree while IQtree upstream decided to name the executable iqtree2. Before I keep on patching I'd like to report this issue to you for further discussion. Kind regards, Andreas.

nickjcroucher commented 1 year ago

Thanks for highlighting @tillea - I think your link is broken though :)

tillea commented 1 year ago

Thanks for highlighting @tillea - I think your link is broken though :)

Argh, fixed. Sorry for that broken advertising (despite that chocolate festival is nice ;-) )

tillea commented 1 year ago

BTW, the patch above is sufficient. First I assumed that there would be more patching needed. However, it was just me who failed to add iqtree to the dependencies of the CI test.

nickjcroucher commented 11 months ago

Are there any further issues that need addressing?

tillea commented 11 months ago

Am Wed, Jul 26, 2023 at 06:26:50AM -0700 schrieb nickjcroucher:

Are there any further issues that need addressing? Not that I'm aware off. Kind regards, Andreas.

nickjcroucher commented 11 months ago

Great, thanks for letting me know!