GIT: Merge branch 'main' into JOSS

metagentools · Sep 18, 2024 · 2c124cd · 2c124cd
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diff --git a/README.md b/README.md
@@ -39,10 +39,10 @@ conda create -n gbintk
 # activate conda environment
 conda activate gbintk
 
-# install graphbin
+# install gbintk
 conda install -c bioconda gbintk
 
-# check graphbin installation
+# check gbintk installation
 gbintk --help
 ```
 
@@ -51,7 +51,11 @@ gbintk --help
 You can install GraphBin-Tk using `pip` from the [PyPI](https://pypi.org/project/gbintk/) distribution.
 
 ```shell
+# install gbintk
 pip install gbintk
+
+# check gbintk installation
+gbintk --help
 ```
 
 ### For development

diff --git a/docs/install.md b/docs/install.md
@@ -2,7 +2,7 @@
 
 GraphBin-Tk is now available on [bioconda](https://anaconda.org/bioconda/gbintk) and [PyPI](https://pypi.org/project/gbintk/).
 
-### Using conda
+## Using conda
 
 You can install GraphBin-Tk using the [bioconda](https://anaconda.org/bioconda/gbintk) distribution. You can download 
 [Anaconda](https://www.anaconda.com/distribution/) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html) which contains `conda`. You can also use [`mamba`](https://mamba.readthedocs.io/en/latest/index.html) instead of `conda`.
@@ -19,17 +19,43 @@ conda create -n gbintk
 # activate conda environment
 conda activate gbintk
 
-# install graphbin
+# install gbintk
 conda install -c bioconda gbintk
 
-# check graphbin installation
+# check gbintk installation
 gbintk --help
 ```
 
-### Using pip
+## Using pip
 
 You can install GraphBin-Tk using `pip` from the [PyPI](https://pypi.org/project/gbintk/) distribution.
 
 ```shell
+# install gbintk
 pip install gbintk
+
+# check gbintk installation
+gbintk --help
+```
+
+## Available subcommands
+
+Run `gbintk --help` or `gbintk -h` to list the help message for GraphBin-Tk.
+
+```shell
+Usage: gbintk [OPTIONS] COMMAND [ARGS]...
+
+  gbintk (GraphBin-Tk): Assembly graph-based metagenomic binning toolkit
+
+Options:
+  -v, --version  Show the version and exit.
+  -h, --help     Show this message and exit.
+
+Commands:
+  graphbin   GraphBin: Refined Binning of Metagenomic Contigs using...
+  graphbin2  GraphBin2: Refined and Overlapped Binning of Metagenomic...
+  metacoag   MetaCoAG: Binning Metagenomic Contigs via Composition,...
+  prepare    Format the initial binning result from an existing binning tool
+  visualise  Visualise binning and refinement results
+  evaluate   Evaluate the binning results given a ground truth
 ```