/GAAS

Genome Assembly and Annotation Service code

Primary LanguagePerlGNU General Public License v3.0GPL-3.0

Build Status install with bioconda Anaconda-Server Badge DOI docker_gaas singularity_gaas Anaconda-Server Badge
GAAS

Genome Assembly Annotation Service (GAAS)

Suite of tools related to Genome Assembly Annotation Service tasks.


Table of Contents


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 part of the repo or if you are looking specifically for genome assembly knowledge The Genome Assembly Workshop Knowledge Base.

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 dependencies<sup>1</sup>
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 dependencies<sup>1</sup>
make                                            # Compile
make test                                       # Test
make install                                    # Install

Uninstall

perl uninstall_GAAS

Usage

script_name.pl -h

Repository structure

Annotation directory contains everything related to annotation side of the service.

Shorcuts:

Assembly directory contains development related to assembly side of the service.

Shorcuts: