diff --git a/README.md b/README.md index 0e59353..65a7242 100644 --- 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 index b0c72a8..abaf895 100644 --- 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 ``` \ No newline at end of file