Git Product home page Git Product logo

genome-assembly-and-annotation-nomenclature_wg's Introduction

Genome Assembly and Gene Model Identifier Tool

This command-line tool facilitates the creation and validation of genome assembly and gene model identifiers based on specific patterns. It is part of the AgBioData Genome Assembly and Annotation Nomenclature Working Group.

Requirements

  • Python 3.x

Installation

To use GAAN, you need to install its dependencies. We recommend using Poetry for managing the project dependencies.

Poetry Installation

If you don't have Poetry installed, you can do so by following the instructions on the official Poetry website.

Install Dependencies

Once Poetry is installed, navigate to the project directory and run the following command to install the dependencies:

poetry install

Usage GAAN provides command-line functionality for creating and validating genome assembly and gene model identifiers. Here are some examples of how to use GAAN:

Create Genome Assembly Identifier

poetry run gaan create-assembly <tol_id> <sample_identifier> <consortium> <version> <subversion> --optional <optional>

Validate Genome Assembly Identifier

poetry run gaan validate-assembly <assembly_id>

Create Gene Model Identifier

poetry run gaan create-gene-model <assembly_prefix> <entity> <id_number>

Validate Gene Model Identifier

poetry run gaan validate-gene-model <gene_model_id>

Replace the placeholders <tol_id>, <sample_identifier>, , , , , <assembly_id>, <assembly_prefix>, , <id_number>, and <gene_model_id> with your specific values.

For more information and options, you can use the --help flag with any of the commands, for example:

poetry run gaan create-assembly --help

Examples

For more examples, refer to the usage section above.

Using Docker (Optional)

If you prefer to use Docker, you can build a Docker image locally. Ensure you have Docker installed on your machine.

# Build the Docker image
docker build -t gaan-tool .

# Run the GAAN tool inside a Docker container
docker run -it gaan-tool [command and arguments]

Replace [command and arguments] with the actual GAAN command and its arguments.

For example:

docker run -it gaan-tool create-assembly ABC123 Sample1 ProjectX 1 0

Note: The Docker image is built locally and not pushed to a container registry. This approach is suitable for local usage.

genome-assembly-and-annotation-nomenclature_wg's People

Contributors

adamjohnwright avatar molikd avatar agbiodata-git avatar

Watchers

 avatar  avatar Sarah Dyer avatar Jacqueline Campbell avatar Jodi Humann avatar

Forkers

molikd

genome-assembly-and-annotation-nomenclature_wg's Issues

dependency installation doesn't work

We have installed poetry (we don't have docker) on the server and I am trying to run the 'poetry install' command from the directory with the files from github and I get the following error:
[tool.poetry] section not found in /u/jhumann/Genome-Assembly-and-Annotation-Nomenclature_WG/pyproject.toml

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.