GAAS

Genome Assembly Annotation Service (GAAS)

Suite of tools related to Genome Assembly Annotation Service tasks.

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Table of Contents

• What can GAAS do for you?
• Installation
  • Using bioconda
    • Install
    • Update
    • Uninstall
  • Old school
    • Prerequisites
    • Install
    • Update
    • Uninstall
    • Change to a specific version
• Usage
• Repository structure

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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

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Repository structure

annotation

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

Shorcuts:

• knowledge

• Genome annotation workshop

• Tools
  => All gff related work have been transplanted into AGAT (11/2019)

• Pipelines

assembly

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

Shorcuts:

• Genome assembly workshop
• The Genome Assembly Workshop Knowledge Base