Florian Plaza Oñate

Hi, Could you add a feature in Jellyfish 2.x which detects output files generated with Jellyfish 1.x? The message "Unknown format'' is not very informative. Thanks in advance.

Use type strains for GTDB to NCBI taxonomy translation

2

Hi, The gtdb_to_ncbi_majority_vote.py is great but is subject to biases when multiple genomes are incorrectly annotated on the NCBI. Have you considered implementing more complex rules such as: 1. Give...

Conda executable crashes

15

Hi @bluenote-1577, I installed sylph using bioconda but it crashed immediately with the following error "Illegal instruction (core dumped)". Notably, the executable available on github works. Best, Florian

Update sylph

2

New attempt to fix issue https://github.com/bluenote-1577/sylph/issues/2 where sylph cannot run on machine embedding a CPU without AVX2 support. This recipes builds binaries for multiple target CPUs and wrapper script automatically...

Cannot build avx512 binaries on Azure

3

Hi, I have written a recipe that generates binaries for different cpu instruction sets: https://github.com/bioconda/bioconda-recipes/pull/50691 Sometimes, the Azure workflow is successful (https://github.com/bioconda/bioconda-recipes/runs/30100279149), sometimes it fails (https://github.com/bioconda/bioconda-recipes/pull/50691/checks?check_run_id=30107543181). When it fails, the...

Add environment variable for mash database

3

Hi, We have installed gtdbtk on our servers but the users do not necessarily know were are the gtdbtk reference data and the mash index. For the gtdbtk reference data,...

Hi, ete3 declares many strings with escape sequences but they are not raw strings. With python 3.12, it generates a SyntaxWarning. Here is the output ``` /usr/local/lib/python3.12/site-packages/ete3/coretype/tree.py:365: SyntaxWarning: invalid escape...