diff --git a/README.md b/README.md index e2de7e5..733012d 100644 --- a/README.md +++ b/README.md @@ -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 ``` Refresh cache and check that everything worked: @@ -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