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Consider:
- get rid of the deprecated submission methods, use publication (methods) instead
- always use the metadata in the submission primary locale
- consider abstract, subjects and keywords (…
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**Description**
After running `bactopia download --build-all envtype conda`, I get an error that the environment cannot be solved.
**Steps to Reproduce**
Steps to reproduce the behavior:
```
(b…
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### Week 1 - Get to know the community
- [x] Join the communication channels
- [x] Open a GitHub issue (this one!)
- [x] Install the Ersilia Model Hub and test the simplest model
- [x] Write a motiva…
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I have a conda environment with AMRFinder+ 3.2.3 but haven't been able to install the database:
```
$ amrfinder -u
Running amrfinder -u
WARNING: Updating database directory works only for databa…
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I've installed a fresh version of bactopia via conda (`mamba create -n bactopia -c conda-forge -c bioconda bactopia`), and now I'm running bactopia datasets to set those up. However, it's returning an…
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### To triage
- [x] [The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages.](https://contribute.data.humancellatlas.org/projects/detail?uuid=4aee283b-ce74-4da6-ade5-d3d…
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Hi!
I would suggest to add the quite popular AMR package, used in many countries to analyse antimicrobial resistance data to help curbing this major global health threat.
On CRAN here: https://…
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**Description**
Hi,
I am having problems downloading MLST schemas for Acinetobacter baumannii. The mlst/oxford/ariba dataset gets only partially downloaded before breaking.
**Steps to reproduce …
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Hi @rpetit3
**Is this something you would like to see added?**
It will be great to have the option `--nanohq` when performing de novo assembly in `bactopia`, just like you did in `dragonflye`!
…
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**Description**
Hello @rpetit3 ,
We are currently using the `shigeifinder` wf in the bactopia tools, but it stucks for many hours. Please find the logs below.
> (base) gilmansiu3@gilmansiu3-Z49…