C. Titus Brown

snakemake should default to `-j 1` when run on command line

4

**Snakemake version** 5.32.2 **Describe the bug** When I install the latest version in a clean environment on Mac OS X or Linux, snakemake insists that I supply `-j/--cores 1`. Per...

WIP: adjust warnings around tax abund and provide v5 upgrades to `tax metagenome`

2

Add new command line arguments to `tax metagenome` around abundances. `--use-abundances` turns on the use of sketch abundances for `krona` and XXX output formats, while `--ignore-abundances/--no-abundances` turns them off. Also...

https://github.com/pyodide/pyodide-recipes/pull/134 ``` ffi.error: symbol 'revindex_free' not found in library '/lib/python3.13/site-packages/sourmash/_lowlevel/lib_lowlevel.so': Tried to lookup unknown symbol "revindex_free" in dynamic lib: /lib/python3.13/site-packages/sourmash/_lowlevel/lib_lowlevel.so ``` My only remaining thought is maybe RocksDB isn't available...

EXP: add bp_weighted_at_rank to tax output

1

NOTE: PR into https://github.com/sourmash-bio/sourmash/pull/3711 Tackles https://github.com/sourmash-bio/sourmash/issues/3313; experimental.

## `sketch` requires multithreading ``` File /lib/python3.12/site-packages/sourmash/utils.py:78, in rustcall(func, *args) 76 if backtrace: 77 exc.rust_info = backtrace ---> 78 raise exc Panic: sourmash panicked: thread 'unnamed' panicked with 'The global...

e.g. see https://github.com/pyodide/pyodide-recipes/pull/134

explore parquet for standalone manifests

2

and/or using polars inside of sourmash

right now if you run `sketch dna` twice, it adds the same sketch twice, and then you have multiple sketches with the same ksizes, which messes up downstream stuff.

Change https://sourmash.readthedocs.io/en/latest/tutorials-lca.html to use sourmash tax.