diff --git a/README.md b/README.md index 55a28d55..98b8ca61 100644 --- a/README.md +++ b/README.md @@ -124,11 +124,9 @@ The external programs that are often used are: - [BEDTOOLS](http://code.google.com/p/bedtools/) - [EMBOSS](http://emboss.sourceforge.net/) -## Installation - -**Installing JCVI in a Conda environment:** +### Managing dependencies with Conda -You can create a Conda environment with Python 3.12 and basic dependencies for JCVI using the YAML files in this repo. +You can use the the YAML files in this repo to create an environment with basic JCVI dependencies. If you are new to Conda, we recommend the [Miniforge](https://conda-forge.org/download/) distribution. @@ -151,8 +149,9 @@ conda activate jcvi-osx64 After activating the Conda environment install JCVI using one of the following options. +## Installation -**Installation options:** +### Installation options 1) Use pip to install the latest development version directly from this repo. @@ -173,7 +172,7 @@ git clone git://github.com/tanghaibao/jcvi.git && cd jcvi pip install -e '.[tests]' ``` -**Test Installation:** +### Test Installation If installed successfully, you can check the version with: @@ -181,6 +180,8 @@ If installed successfully, you can check the version with: jcvi --version ``` +## Usage + Use `python -m` to call any of the modules installed with JCVI. Most of the modules in this package contains multiple actions. To use