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Merge branch 'main' into frequency_table_branched_from_main after PRs
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@VinzentRisch
VinzentRisch committed Jan 4, 2024
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Expand Up @@ -10,16 +10,15 @@ To install _q2-amr_, follow the installation steps described below.

```shell
mamba create -yn q2-amr \
-c conda-forge -c bioconda -c qiime2 -c defaults \
-c https://packages.qiime2.org/qiime2/2023.5/tested \
--no-channel-priority \
qiime2 q2cli q2templates q2-types q2-types-genomics rgi altair
-c conda-forge -c bioconda -c qiime2 -c defaults \
-c https://packages.qiime2.org/qiime2/2023.9/shotgun/released/ \
qiime2 q2cli q2templates q2-types q2-types-genomics rgi altair

conda activate q2-amr

pip install --no-deps --force-reinstall \
git+https://github.com/misialq/rgi.git@py38-fix \
git+https://github.com/bokulich-lab/q2-amr.git
git+https://github.com/misialq/rgi.git@py38-fix \
git+https://github.com/bokulich-lab/q2-amr.git
```

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Expand All @@ -34,13 +33,13 @@ sequencing reads and MAGs with antimicrobial resistance genes. Currently, the [C
the implementation and usage, please refer to the [rgi](https://github.com/arpcard/rgi) documentation). Below you will
find an overview of actions available in the plugin.

| Action | Description | Underlying tool |
|----------------------------|--------------------------------------------------------------------------------------|---------------------------------------|
| fetch-card-db | Download CARD data. | [rgi](https://github.com/arpcard/rgi) |
| annotate-mags-card | Annotate MAGs with antimicrobial resistance gene information from CARD. | [rgi](https://github.com/arpcard/rgi) |
| annotate-reads-card | Annotate metagenomic reads with antimicrobial resistance gene information from CARD. | [rgi](https://github.com/arpcard/rgi) |
| heatmap | Create a heatmap from annotate-mags-card output files. | |
| visualize-annotation-stats | Plot annotate-reads-card annotation statistics. | |
| Action | Description | Underlying tool | Used function |
|----------------------------|--------------------------------------------------------------------------------------|---------------------------------------|--------------------------------------|
| fetch-card-db | Download and preprocess CARD and WildCARD data. | [rgi](https://github.com/arpcard/rgi) | card_annotation, wildcard_annotation |
| annotate-mags-card | Annotate MAGs with antimicrobial resistance gene information from CARD. | [rgi](https://github.com/arpcard/rgi) | main, load |
| annotate-reads-card | Annotate metagenomic reads with antimicrobial resistance gene information from CARD. | [rgi](https://github.com/arpcard/rgi) | bwt, load |
| heatmap | Create a heatmap from annotate-mags-card output files. | [rgi](https://github.com/arpcard/rgi) | heatmap |
| visualize-annotation-stats | Plot annotate-reads-card annotation statistics. | | |


## Dev environment
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