Hymenium

Trinity exits immediately if the read files are passed alongside the aligned reads bam file in genome guided mode. - Problem already identified here: https://help.galaxyproject.org/t/genome-guided-trinity-bug-with-both-fastq-and-bam-files/11771 - The older Trinity 2.9.1+galaxy1...

MitoHiFi defaulting to animal data

1

tools/mitohifi/mitohifi.xml I didn't realise from the help that this tool is designed for and defaulting to animal data. When I tried with fungal data then all of the blast matches...

The export option exports the current view and it is impossible to fit a moderately sized tree or network. Please could you add an option to export the full image,...

I have tried using GTR and K2P to calculate distances but the results are strange and give very strange splits. I have checked against distances using the same models in...

BUSCO gff file(s) not captured in output when Augustus used, no errors as stderr suppressed

2

Despite >90% of BUSCOs being matched in a genome, the buso_output.gff file is empty. I'm not sure why this cat command doesn't get the contents of the .gff files. The...

I am getting an error from the raxml.py code if I try to use the 'estimate individual per-partition branch length (-M)' in RAxML. It seems like these partition files are...

Unclear explanation and options for Funannotate --augustus_species parameter

4

The --augustus_species parameter in Funannotate appears to be for reusing Augustus training sets from previous runs of Funannotate. I'm not sure if this data is kept from one run to...

Godot: Inconsistent behaviour for the one-way collision margin parameter of CollisionPolygon2D

3

**Describe the bug** - inconsistent behaviour with Godot 2D engine In Godot, a CollisionPolygon2D object has a one-way collision margin parameter (https://docs.godotengine.org/en/stable/classes/class_collisionpolygon2d.html#class-collisionpolygon2d-property-one-way-collision-margin), defaulting to one pixel. This parameter seems to...

Alternative compile options for clang-cl with MSVC driver

2

This PR offers an alternative to #995 for Windows builds with LLVM clang-cl and the MSVC driver. - ```/Wall``` with the MSVC driver seems very broad, and results in more...

Update SGP and samples to use new SGL views API

1

Following #52 and #50, this PR updates **sokol_gp** to the latest sokol headers and migrates image usage to the new *views* API with minimal changes. **What's changed:** - Sokol headers...