{"repo":"rhysnewell/aviary","free":true,"listed":false,"github":"https://github.com/rhysnewell/aviary","clone":"git clone https://github.com/rhysnewell/aviary.git","description":"A hybrid assembly and MAG recovery pipeline (and more!)","language":"Python","stars":116,"topics":["assembly","binning","bioinformatics","metagenomics","workflow"],"license":"GPL-3.0","category":"workflow-automation","readme_excerpt":"Aviary An easy to use for wrapper for a robust snakemake pipeline for metagenomic short-read, long-read, and hybrid assembly. Aviary also performs binning, annotation, and provides users with an easy way to combine and dereplicate many aviary results with rapidity. The pipeline currently includes a series of distinct, yet flexible, modules that can seamlessly communicate with each other. Each module can be run independently or as a single pipeline depending on provided input. Please refer to the full docs here Quick Installation Your conda channels should be configured ideally in this order: Your resulting .condarc file should look something like: Option 1: Install from Bioconda Conda can handle the creation of the environment for you directly: Or install into existing environment: Option 2: Install from pip Create the environment using the admin/requirements.txt file then install from pip: Option 3: Install from source This method can be somewhat complicated, as you can see below, but it allows for easier/faster development and debugging of aviary itself. Clone To install from source, we recommend using pixi. First clone the aviary repository from GitHub: Create aviary/.pixi (possibly symlinked to faster disk) In the source directory, create the aviary/.pixi directory to hold pixi environments. Without this, .pixi is symlinked to aviary/.pixi within the checkout, which does not exist. So pixi run .. trips over that dead link. This can be done by simply running: Post-installa","default_branch":null,"files":null,"tree":[],"storefront":"/r/rhysnewell","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/rhysnewell/aviary/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}