{"id":25977386,"url":"https://github.com/nbisweden/gaas","last_synced_at":"2025-04-03T03:13:30.419Z","repository":{"id":14589643,"uuid":"53501201","full_name":"NBISweden/GAAS","owner":"NBISweden","description":"Genome Assembly and Annotation Service code","archived":false,"fork":false,"pushed_at":"2023-12-18T08:42:30.000Z","size":30745,"stargazers_count":210,"open_issues_count":10,"forks_count":47,"subscribers_count":51,"default_branch":"master","last_synced_at":"2025-03-26T20:12:22.049Z","etag":null,"topics":["annotation","assembly","cheatsheet","knowledge","scripts"],"latest_commit_sha":null,"homepage":"","language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/NBISweden.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-03-09T13:49:35.000Z","updated_at":"2025-03-25T20:12:17.000Z","dependencies_parsed_at":"2025-03-05T04:44:09.470Z","dependency_job_id":null,"html_url":"https://github.com/NBISweden/GAAS","commit_stats":null,"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NBISweden%2FGAAS","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NBISweden%2FGAAS/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NBISweden%2FGAAS/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NBISweden%2FGAAS/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/NBISweden","download_url":"https://codeload.github.com/NBISweden/GAAS/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246927839,"owners_count":20856198,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["annotation","assembly","cheatsheet","knowledge","scripts"],"created_at":"2025-03-05T04:34:01.188Z","updated_at":"2025-04-03T03:13:30.393Z","avatar_url":"https://github.com/NBISweden.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Build Status](https://travis-ci.org/NBISweden/GAAS.svg?branch=master)](https://travis-ci.org/NBISweden/GAAS)\n[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/gaas/README.html)\n[![Anaconda-Server Badge](https://img.shields.io/conda/dn/bioconda/gaas.svg?style=flat)](https://anaconda.org/bioconda/gaas)\n[![DOI](https://zenodo.org/badge/53501201.svg)](https://zenodo.org/badge/latestdoi/53501201)\n[\u003cimg alt=\"docker_gaas\" src=\"https://img.shields.io/badge/container-Docker-blue\"\u003e](https://quay.io/repository/biocontainers/gaas)\n[\u003cimg alt=\"singularity_gaas\" src=\"https://img.shields.io/badge/container-Singularity-orange\"\u003e](https://quay.io/repository/biocontainers/gaas)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/gaas/badges/license.svg)](https://anaconda.org/bioconda/gaas)   \nGAAS \n=========================================\n\u003ch2\u003e\u003cem\u003eG\u003c/em\u003eenome \u003cem\u003eA\u003c/em\u003essembly \u003cem\u003eA\u003c/em\u003ennotation \u003ci\u003eS\u003c/i\u003eervice (GAAS)\u003c/h2\u003e  \nSuite of tools related to Genome Assembly Annotation Service tasks.\n\n[\u003cimg align=\"right\" src=\"NBIS.png\" width=\"200\" height=\"100\" /\u003e](https://nbis.se)\n\n---------------------------\n\n## Table of Contents\n\n   * [What can GAAS do for you?](#what-can-gaas-do-for-you)\n   * [Installation](#installation)  \n       * [Using bioconda](using-bioconda)\n          * [Install](#install)\n          * [Update](#update)\n          * [Uninstall](#uninstall)\n       * [Old school](#old-school)\n          * [Prerequisites](#prerequisites)\n          * [Install](#install-1)\n          * [Update](#update-1)\n          * [Uninstall](#uninstall-1)\n          * [Change to a specific version](#change-to-a-specific-version)\n   * [Usage](#usage)\n   * [Repository structure](#repository-structure)\n\n---------------------------\n\n## What can GAAS do for you?  \n\nThe repository contains mainly tools and knowledge related to bioinformatics and annotation the most often. To access and install the tools please follow the installation procedures below. For the knowledge you are invited to visit the [knowledge](annotation/knowledge) part of the repo or if you are looking specifically for genome assembly knowledge [The Genome Assembly Workshop Knowledge Base](https://github.com/NBISweden/workshop-genome_assembly/wiki).\n\n## Installation\n\n### Using conda\n\n#### Install\n\n  ```\n  conda install -c bioconda gaas\n  ```\n\n#### Update\n\n  ```\n  conda update gaas\n  ```\n\n#### Uninstall\n  ```\n  conda uninstall gaas  \n  ```\n\n### Old school\n\n#### Prerequisites\n  * R\n  * Perl\n    Perl \u003e= 5.8, and a list of perl modules that can be installed using cpan, cpanm or conda:\n\n    * Install perl modules with cpanm\n    ```\n    cpanm install bioperl\n    cpanm install Clone\n    cpanm install Graph::Directed\n    cpanm install LWP::UserAgent\n    cpanm install Statistics::R\n    cpanm install Sort::Naturally\n    cpanm install File::Share\n    cpanm install Moose\n    cpanm install File::ShareDir::Install\n    cpanm install Bio::DB::EUtilities\n    ```\n    * Install perl modules with conda\n\n    ```\n    conda env create -f conda_environment_GAAS.yml\n    conda activate gaas\n    ```\n\n#### Install\n\n  ```\n  git clone https://github.com/NBISweden/GAAS.git # Clone GAAS\n  cd GAAS                                         # move into GAAS folder\n  perl Makefile.PL                                # Check all the dependencies*\n  make                                            # Compile\n  make test                                       # Test\n  make install                                    # Install\n  ```\n\n\u003csup\u003e*\u003c/sup\u003eIf dependencies are missing you can install them using cpan/cpanm or use conda and load the environment conda_environment_GAAS.yml\n\n**Remark**: On MS Windows, instead of make you'd probably have to use dmake or nmake depending the toolchain you have.\n\n#### Update  \nFrom the folder where the repository is located.\n\n  ```\n  git pull                                        # Update to last GAAS\n  perl Makefile.PL                                # Check all the dependencies\u003csup\u003e1\u003c/sup\u003e\n  make                                            # Compile\n  make test                                       # Test\n  make install                                    # Install\n  ```\n\n#### Change to a specific version\nFrom the folder where the repository is located.  \n\n  ```\n  git pull                                        # Update the code\n  git checkout v0.1.1                             # use version v0.1 (See releases tab for a list of available versions)\n  perl Makefile.PL                                # Check all the dependencies\u003csup\u003e1\u003c/sup\u003e\n  make                                            # Compile\n  make test                                       # Test\n  make install                                    # Install\n  ```\n\n#### Uninstall\n\n  ```\n  perl uninstall_GAAS\n  ```\n\n## Usage\n\n  ```\n  script_name.pl -h\n  ```    \n  \n---------------------------\n\n## Repository structure\n\n## [__annotation__](annotation)  \nAnnotation directory contains everything related to annotation side of the service.  \n\n#### Shorcuts:  \n   - [knowledge](annotation/knowledge)\n\n   - [Genome annotation workshop](https://nbisweden.github.io/workshop-genome_annotation/)\n\n   - [Tools](annotation/tools)  \n     =\u003e All gff related work have been transplanted into [AGAT](https://github.com/NBISweden/AGAT) (11/2019)\n\n   - [Pipelines](https://github.com/NBISweden/pipelines-nextflow)\n\n## [__assembly__](assembly)  \nAssembly directory contains development related to assembly side of the service.  \n\n#### Shorcuts:  \n   - [Genome assembly workshop](https://nbisweden.github.io/workshop-genome_assembly/)\n   - [The Genome Assembly Workshop Knowledge Base](https://github.com/NBISweden/workshop-genome_assembly/wiki)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnbisweden%2Fgaas","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnbisweden%2Fgaas","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnbisweden%2Fgaas/lists"}