Byron J. Smith

Reasonable caching of downloaded conda packages when --use-conda and --use-singularity together

2

**Is your feature request related to a problem? Please describe.** Installing conda environments can be slow, which makes troubleshooting a problematic one very frustrating. It would be nice if package...

List location in info summary box at top of the main page.

4

I usually end up adding the workshop location to the info box at the top of the page, so that learners don't need to scan for it in the "General...

Is this the expected behavior of patsy when building a design matrix of a two-level categorical variable without an intercept?

12

cloned from stackoverflow: http://stackoverflow.com/questions/35944841/is-this-the-expected-behavior-of-patsy-when-building-a-design-matrix-of-a-two-le (patsy v0.4.1, python 3.5.0) I would like to use patsy (ideally through statsmodels) to build a design matrix for regression. The patsy-style formula that I would...

Bad behavior on collapse/cartoon at deepest binary split.

1

When I select a group one level away from the root (for instance, an outgroup) and press either "Cartoon" or "Collapse", the entire tree is affected, instead of just the...

Terminate called after throwing an instance of 'std::runtime_error'; Unable to open superkmers/xjin_AB_P0R2c/skp.90

2

I'm getting the following error when I run kmtricks with 276 samples: ``` $ kmtricks pipeline --kmer-size 111 --hard-min 0 --share-min 1 --soft-min 2 --recurrence-min 3 --file data/group/xjin/r.proc.kmtricks_input.txt --run-dir --mode...

`snakemake --touch` is slow/handicapped for unclear reasons

1

**Snakemake version**: 7.25.4 (but has not been fixed in the main branch, unless I'm misunderstanding something) **Describe the bug** When I want to "clean up" a large workflow (e.g. to...