https://github.com/nbisweden/gaas
Genome Assembly and Annotation Service code
https://github.com/nbisweden/gaas
annotation assembly cheatsheet knowledge scripts
Last synced: 3 months ago
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Genome Assembly and Annotation Service code
- Host: GitHub
- URL: https://github.com/nbisweden/gaas
- Owner: NBISweden
- License: gpl-3.0
- Created: 2016-03-09T13:49:35.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2023-12-18T08:42:30.000Z (over 1 year ago)
- Last Synced: 2025-03-26T20:12:22.049Z (3 months ago)
- Topics: annotation, assembly, cheatsheet, knowledge, scripts
- Language: Perl
- Homepage:
- Size: 29.3 MB
- Stars: 210
- Watchers: 51
- Forks: 47
- Open Issues: 10
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
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README
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[](http://bioconda.github.io/recipes/gaas/README.html)
[](https://anaconda.org/bioconda/gaas)
[](https://zenodo.org/badge/latestdoi/53501201)
[
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](https://quay.io/repository/biocontainers/gaas)
[](https://anaconda.org/bioconda/gaas)
GAAS
=========================================
Genome Assembly Annotation Service (GAAS)
Suite of tools related to Genome Assembly Annotation Service tasks.
[
](https://nbis.se)
---------------------------
## Table of Contents
* [What can GAAS do for you?](#what-can-gaas-do-for-you)
* [Installation](#installation)
* [Using bioconda](using-bioconda)
* [Install](#install)
* [Update](#update)
* [Uninstall](#uninstall)
* [Old school](#old-school)
* [Prerequisites](#prerequisites)
* [Install](#install-1)
* [Update](#update-1)
* [Uninstall](#uninstall-1)
* [Change to a specific version](#change-to-a-specific-version)
* [Usage](#usage)
* [Repository structure](#repository-structure)
---------------------------
## What can GAAS do for you?
The 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).
## Installation
### Using conda
#### Install
```
conda install -c bioconda gaas
```
#### Update
```
conda update gaas
```
#### Uninstall
```
conda uninstall gaas
```
### Old school
#### Prerequisites
* R
* Perl
Perl >= 5.8, and a list of perl modules that can be installed using cpan, cpanm or conda:
* Install perl modules with cpanm
```
cpanm install bioperl
cpanm install Clone
cpanm install Graph::Directed
cpanm install LWP::UserAgent
cpanm install Statistics::R
cpanm install Sort::Naturally
cpanm install File::Share
cpanm install Moose
cpanm install File::ShareDir::Install
cpanm install Bio::DB::EUtilities
```
* Install perl modules with conda
```
conda env create -f conda_environment_GAAS.yml
conda activate gaas
```
#### Install
```
git clone https://github.com/NBISweden/GAAS.git # Clone GAAS
cd GAAS # move into GAAS folder
perl Makefile.PL # Check all the dependencies*
make # Compile
make test # Test
make install # Install
```
*If dependencies are missing you can install them using cpan/cpanm or use conda and load the environment conda_environment_GAAS.yml
**Remark**: On MS Windows, instead of make you'd probably have to use dmake or nmake depending the toolchain you have.
#### Update
From the folder where the repository is located.
```
git pull # Update to last GAAS
perl Makefile.PL # Check all the dependencies1
make # Compile
make test # Test
make install # Install
```
#### Change to a specific version
From the folder where the repository is located.
```
git pull # Update the code
git checkout v0.1.1 # use version v0.1 (See releases tab for a list of available versions)
perl Makefile.PL # Check all the dependencies1
make # Compile
make test # Test
make install # Install
```
#### Uninstall
```
perl uninstall_GAAS
```
## Usage
```
script_name.pl -h
```
---------------------------
## Repository structure
## [__annotation__](annotation)
Annotation directory contains everything related to annotation side of the service.
#### Shorcuts:
- [knowledge](annotation/knowledge)
- [Genome annotation workshop](https://nbisweden.github.io/workshop-genome_annotation/)
- [Tools](annotation/tools)
=> All gff related work have been transplanted into [AGAT](https://github.com/NBISweden/AGAT) (11/2019)
- [Pipelines](https://github.com/NBISweden/pipelines-nextflow)
## [__assembly__](assembly)
Assembly directory contains development related to assembly side of the service.
#### Shorcuts:
- [Genome assembly workshop](https://nbisweden.github.io/workshop-genome_assembly/)
- [The Genome Assembly Workshop Knowledge Base](https://github.com/NBISweden/workshop-genome_assembly/wiki)